Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

Performance Evaluation of Developed Bangasure™ Multiplex rRT-PCR Assay for SARS-CoV-2 Detection in Bangladesh: A Blinded Observational Study at Two Different Sites

In this study, we evaluated the performance of the in-house developed rRT-PCR assay for SARS-CoV-2 RNA targeting the envelope (E) and nucleocapsid (N) genes with internal control as human RNase P. A total of 50 positive samples and 50 negative samples of SARS-CoV-2 were tested by a reference kit at site 1 and a subset (30 positives and 16 negatives) of these samples are tested blindly at site 2. The limit of detection (LoD) was calculated by using a replication-deficient complete SARS-CoV-2 genome and known copy numbers, where Pseudo-virus samples were used to evaluate accuracy. On site 1, among the 50 SARS-CoV-2 positive samples 24, 18, and eight samples showed high (Ct < 26), moderate (26 < Ct ≤ 32), and low (32 < Ct ≤ 38) viral load, respectively, whereas in site 2, out of 30 SARS-CoV-2 positive samples, high, moderate, and low viral loads were found in each of the 10 samples. However, SARS-CoV-2 was not detected in the negative sample. So, in-house assays at both sites showed 100% sensitivity and specificity with no difference observed between RT PCR machines. The Ct values of the in-house kit had a very good correlation with the reference kits. LoD was determined as 100 copies/mL. It also displayed 100% accuracy in mutant and wild-type SARS-CoV-2 virus. This Bangasure™ RT-PCR kit shows excellent performance in detecting SARS-CoV-2 viral RNA compared to commercially imported CE-IVD marked FDA authorized kits.

TEMPOL inhibits SARS-CoV-2 replication and development of lung disease in the Syrian hamster model

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide outbreak, known as coronavirus disease 2019 (COVID-19). Alongside vaccines, antiviral therapeutics is an important part of the healthcare response to COVID-19. We previously reported that TEMPOL, a small molecule stable nitroxide, inactivated the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by causing the oxidative degradation of its iron-sulfur cofactors. Here, we demonstrate that TEMPOL is effective in vivo in inhibiting viral replication in the Syrian hamster model. The inhibitory effect of TEMPOL on SARS-CoV-2 replication was observed in animals when the drug was administered 2 h before infection in a high-risk exposure model. These data support the potential application of TEMPOL as a highly efficacious antiviral against SARS-CoV-2 infection in humans.

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TEMPOL’s IC₉₀ in human lung epithelial Calu-3 cells is 2.89 μM and CC₅₀ > 10 mM

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TEMPOL has potent antiviral activity against highly pathogenic SARS- and MERS-Co-Vs

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TEMPOL inhibits SARS-CoV-2 replication and lung pathology in the Syrian hamster

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Fe-S cofactor insertion can be targeted to interfere with coronavirus replication

When to test for COVID-19 using real-time reverse transcriptase polymerase chain reaction: a systematic review

OBJECTIVES

The aim of this study was to evaluate the time in days between symptom onset and first positive real-time reverse transcriptase polymerase chain reaction (RT-PCR) result for COVID-19.

METHODS

This systematic review was conducted in the MEDLINE (PubMed), Embase, and Scopus databases using the following descriptors: "COVID-19", "SARS-CoV-2", "coronavirus", "RT-PCR", "real time PCR", and "diagnosis".

RESULTS

The included studies were conducted in 31 different countries and reported on a total of 6831 patients. The median age of the participants was 49.95 years. The three most common symptoms were fever, cough, and dyspnea, which affected 4012 (58.68%), 3192 (46.69%), and 2009 patients (29.38%), respectively. Among the 90 included studies, 13 were prospective cohorts, 15 were retrospective cohorts, 36 were case reports, 20 were case series, and six were cross-sectional studies. The overall mean time between symptom onset and positive test result was 6.72 days. Fourteen articles were analyzed separately for the temporal profile of RT-PCR test results; the best performance was on days 22-24, when 98% of test results were positive.

CONCLUSION

These findings corroborate the RT-PCR COVID-19 testing practices of some health units. In addition, the most frequently described symptoms of these patients can be considered the initial symptoms of infection and used in decision-making about RT-PCR testing.

SARS-CoV-2 detection methods: A comprehensive review

The ongoing novel COVID-19 has remained the center of attention, since its declaration as a pandemic in March 2020, due to its rapid and uncontrollable worldwide spread. Diagnostic tests are the first line of defense against the transmission of this infectious disease among individuals, with reverse-transcription quantitative polymerase chain reaction (RT-qPCR) being the approved gold standard for showing high sensitivity and specificity in detecting SARS-CoV-2. However, alternative tests are being invested due to the global demand for facilities, reagents, and healthcare workers needed for rapid population-based testing. Also, the rapid evolution of the viral genome and the emergence of new variants necessitates updating the existing methods. Scientists are aiming to improve tests to be affordable, simple, fast, and at the same time accurate, and efficient, as well as friendly user testing. The current diagnostic methods are either molecular-based that detect nucleic acids abundance, like RT-qPCR and reverse-transcription loop-mediated isothermal amplification (RT-LAMP); or immunologically based that detect the presence of antigens or antibodies in patients’ specimens, like enzyme-linked immunosorbent assay (ELISA), lateral flow assay (LFA), chemiluminescent immunoassay (CLIA), and neutralization assay. In addition to these strategies, sensor-based or CRISPR applications are promising tools for the rapid detection of SARS-CoV-2. This review summarizes the most recent updates on the SARS-CoV-2 detection methods with their limitations. It will guide researchers, epidemiologists, and clinicians in identifying a more rapid, reliable, and sensitive method of diagnosing SARS-CoV-2 including the most recent variant of concern Omicron.

Relevance of cycle threshold values in mass screening by reverse-transcription-PCR during COVID-19 pandemic in Belgium: a decision-making support?

Aim: The Belgium’s strategy against COVID-19 was partly based on mass screening. Here, we reported the results observed in a Belgian mass screening center. Materials & methods: Between October 2020 and February 2021, 32,089 samples were collected analyzed with reverse-transcription PCR (Thermo Fisher Scientific kits and apparatus). Patients were categorized according to their contagiousness (extrapolated from the cycle threshold [Ct] values and the recommendation of Sciensano). Results: We observed association between Ct values and age, with higher Ct observed in extreme age groups (<6 years and >75 years). Conclusion: The analysis of the evolution of the contagiousness of these patients tested twice within a 7-day period showed the relevancy of the recommendation edited by Sciensano.

The Belgium’s strategy against COVID-19 was partly based on mass screening performed with reverse-transcription PCR analysis performed on nasopharyngeal samples. Reverse-transcription PCR allows the detection of individuals infected by the virus. In addition, it provides semi quantitative results correlated to the quantity of virus present in the patient, these results are difficult to interpret for the patients and numerous practitioners. In our study, we showed that the interpretation of these results should take into account the age of the patients. We also showed that the semi quantitative result observed in a positive patient is not predictive of the evolution of the viral load (quantity of virus present in the organism) in the 7 following days.

The Multifaceted Relationship between the COVID-19 Pandemic and the Food System

The SARS-CoV-2 pandemic is being questioned for its possible food transmission, due to several reports of the virus on food, outbreaks developed in food companies, as well as its origins linked to the wet market of Wuhan, China. The purpose of this review is to analyze the scientific evidence gathered so far on the relationship between food and the pandemic, considering all aspects of the food system that can be involved. The collected data indicate that there is no evidence that foods represent a risk for the transmission of SARS-CoV-2. In fact, even if the virus can persist on food surfaces, there are currently no proven cases of infection from food. Moreover, the pandemic showed to have deeply influenced the eating habits of consumers and their purchasing methods, but also to have enhanced food waste and poverty. Another important finding is the role of meat processing plants as suitable environments for the onset of outbreaks. Lessons learned from the pandemic include the correct management of spaces, food hygiene education for both food workers and common people, the enhancement of alternative commercial channels, the reorganization of food activities, in particular wet markets, and intensive farming, following correct hygiene practices. All these outcomes lead to another crucial lesson, which is the importance of the resilience of the food system. These lessons should be assimilated to deal with the present pandemic and possible future emergencies. Future research directions include further investigation of the factors linked to the food system that can favor the emergence of viruses, and of innovative technologies that can reduce viral transmission.

A comprehensive review of BBV152 vaccine development, effectiveness, safety, challenges, and prospects

The world has responded to the COVID-19 pandemic with unprecedented speed and vigor in the mass vaccination campaigns, targeted to reduce COVID-19 severity and mortality, reduce the pressure on the healthcare system, re-open society, and reduction in disease mortality and morbidity. Here we review the preclinical and clinical development of BBV152, a whole virus inactivated vaccine and an important tool in the fight to control this pandemic. BBV152, formulated with a TLR7/8 agonist adjuvant generates a Th1-biased immune response that induces high neutralization efficacy against different SARS-CoV-2 variants of concern and robust long-term memory B- and T-cell responses. With seroconversion rates as high as 98.3% in vaccinated individuals, BBV152 shows 77.8% and 93.4% protection from symptomatic COVID-19 disease and severe symptomatic COVID-19 disease respectively. Studies in pediatric populations show superior immunogenicity (geometric mean titer ratio of 1.76 compared to an adult) with a seroconversion rate of >95%. The reactogenicity and safety profiles were comparable across all pediatric age groups between 2-18 yrs. as in adults. Like most approved vaccines, the BBV152 booster given 6 months after full vaccination, reverses a waning immunity, restores the neutralization efficacy, and shows synergy in a heterologous prime-boost study with about 3-fold or 300% increase in neutralization titers against multiple SARS-CoV-2 variants of concern. Based on the interim Phase III data, BBV152 received full authorization for adults and emergency use authorization for children from ages 6 to 18 years in India. It is also licensed for emergency use in 14 countries globally. Over 313 million vaccine doses have already been administered in India alone by April 18th, 2022.

Colorimetric and fluorometric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for diagnosis of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since it infected humans almost 3 years ago. Improvements of current assays and the development of new rapid tests or to diagnose SARS-CoV-2 are urgent. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and propitious assay, allowing to detect both colorimetric and/or fluorometric nucleic acid amplifications. This study describes the analytical and clinical evaluation of RT-LAMP assay for detection of SARS-CoV-2, by designing LAMP primers targeting N (nucleocapsid phosphoprotein), RdRp (polyprotein), S (surface glycoprotein), and E (envelope protein) genes. The assay’s performance was compared with the gold standard RT-PCR, yielding 94.6% sensitivity and 92.9% specificity. Among the tested primer sets, the ones for S and N genes had the highest analytical sensitivity, showing results in about 20 min. The colorimetric and fluorometric comparisons revealed that the latter is faster than the former. The limit of detection (LoD) of RT-LAMP reaction in both assays is 50 copies/µl of the reaction mixture. However, the simple eye-observation advantage of the colorimetric assay (with a color change from yellow to red) serves a promising on-site point-of-care testing method anywhere, including, for instance, laboratory and in-house applications.

An overview of gastrointestinal diseases in patients with COVID-19: A narrative review

Coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), has emerged as a global health concern. This study aimed to review the epidemiology and pathophysiology of COVID-19 and provide evidence for the implementation of control measures. We utilized several online databases, including MEDLINE (National Library of Medicine, Bethesda, Maryland, USA), PubMed, EMBASE, Web of Science, and Google Scholar, to collect relevant published papers using a combination of the following keywords: "COVID-19," "SARS-CoV-2," "novel coronavirus," "epidemiology," and "pathophysiology." The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were used in this study. Globally, approximately 3-46% of patients with SARS-CoV-2 infection experience gastrointestinal symptoms. The clinical spectrum of COVID-19 is wide, ranging from mild to severe, and even fatal. COVID-19 was initially reported as a respiratory tract disease; however, gastrointestinal symptoms have only recently been reported. COVID-19 Patients with gastrointestinal symptoms may have more severe clinical manifestations and poor prognosis. This study highlights the need to better understand the mechanisms involved in the development of gastrointestinal symptoms in patients with COVID-19 to prevent the further spread of this pathogen.

RT-PCR Ct values combined with age predicts invasive mechanical ventilation and mortality in hospitalized COVID-19 patients in a MERS-CoV-endemic country

Background

Several risk factors have been used to predict severity of coronavirus disease 2019 (COVID-19), real-time reverse transcriptase polymerase chain reaction (RT-PCR) cycle threshold (Ct) values have not been included.

Methods

A retrospective analysis of laboratory-confirmed COVID-19 patients who were hospitalized between March 2 and September 1, 2020, in an academic hospital in Riyadh that serves as a Middle East respiratory syndrome coronavirus (MERS-CoV) referral center was conducted. Nasopharyngeal (NP) and endotracheal (ET) samples were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by RT-PCR, and viral load (VL) was determined based on the Ct values of E genes. The Ct values were distributed into four groups, with group Ct1 (≤19) indicating the highest VL and Ct4 (≥31) indicating the lowest VL. Univariate logistic regression was used to analyze age, gender, and comorbidities in relation to Ct groups for a primary endpoint of either invasive mechanical ventilation (IMV) or mortality. Significant variables were further analyzed by multivariate logistic regression.

Results

The analysis included 728 patients hospitalized with COVID-19 (38% female; median age = 53 years; 41.3% diabetic; 39.4% hypertensive). Overall, 13.6% of these patients required IMV, and the in-hospital mortality rate was 15.5%. The IMV rate was higher in the Ct1 and Ct2 groups (15.2% and 15.5%, respectively) than in the Ct4 group (6.4%; p = 0.01). The mortality rate was also higher in the Ct1 and Ct2 groups (19.4% and 18.9%, respectively) than in the Ct4 group (8.9%; p = 0.02). The univariate analysis showed that lower Ct values and increasing age were associated with an increased risk of IMV (OR: 1.03; 95% CI: 1.01, 1.04; P < 0.0001) and mortality (OR: 1.04; 95% CI: 1.03, 1.06; P < 0.0001). The multivariate analysis showed that Ct1 was associated with the highest risk of mortality (OR: 2.29; 95% CI: 1.16, 5.52; P = 0.016), while Ct2 was associated with the highest risk of IMV (OR: 3.1; 95% CI: 1.47, 6.53; P = 0.003).

Conclusion

The SARS-CoV-2 RT-PCR Ct values of hospitalized COVID-19 patients can be used as predictors of IMV and mortality, and this effect increases when combined with age. Clinicians could use these predictors to triage older patients for risk stratification and allocate IMV.

High sensitivity detection of SARS-CoV-2 by an optofluidic hollow eccentric core fiber

Since the outbreak of coronavirus disease 2019 (COVID-19), efficient real-time monitoring has become one of the challenges faced in SARS-CoV-2 virus detection. A compact all-fiber Mach-Zehnder interferometer optofluidic sensor based on a hollow eccentric core fiber (HECF) for the detection and real-time monitoring of SARS-CoV-2 spike glycoprotein (SARS-CoV-2 S2) is proposed, analyzed and demonstrated. The sensor is comprised of fusion splicing single mode fiber (SMF), hollow core fiber (HCF) and HECF. After the incident light passes through the HCF from the SMF, it uniformly enters the air hole and the suspended micrometer-scale fiber core of the HECF to form a compact all-fiber Mach-Zehnder interferometer (MZI). HECF is side polished to remove part of the cladding that the suspended fiber core can contact the external environment. Subsequently, the mouse anti SARS-CoV-2 S2 antibody is fixed on the surface of the suspended-core for the sake of achieving high sensitivity and specific sensing of SARS-CoV-2 S2. The limit of detection (LOD) of the sensor is 26.8 pM. The proposed sensor has high sensitivity, satisfactory selectivity, and can be fabricated at low cost making it highly suitable for point-of-care testing and high-throughput detection of early stage of COVID-19 infection.

Digital RT-PCR Chip method for detection of SARS-CoV-2 virus

The “gold standard” method for detection of SARS-CoV-2 is the real time reverse transcription-polymerase chain reaction, but due to pre-analytical and technical limitations, biological samples with low viral load are not sometimes detected. For this purpose a digital RT-PCR method on-chip was developed for detection of the SARS-CoV-2 virus, using two TaqMan™ Assays for quantification of the N Protein (Nucleocapsid) and the S Protein (Spike), and the QuantStudio™ 3D Digital PCR instrument. The method was applied to assess the nasopharyngeal swabs of asymptomatic subjects recruited in the UNICORN Study. The digital RT-PCR method is characterized by a higher sensitivity than the RT-qPCR method, even if performed with the same TaqMan™, and could be a promising tool for SARS-CoV-2 viral load quantification.

Current status and capacity of pathogen laboratories in centers for disease control and prevention in China during the COVID-19 pandemic: A nationwide cross-sectional survey

The pathogen laboratory (p-lab) is the core and primary department of centers for disease control and prevention (CDCs) in China to respond to infectious disease outbreaks such as COVID-19. To understand the current status and capacity of p-labs in Chinese CDCs during the COVID-19 pandemic, we conducted a nationwide cross-sectional survey among 399 respondents from 239 CDCs. Differences in the current status of p-labs in CDCs of provinces, cities, and counties mainly comprised laboratory equipment, IEIs, mastery of personal occupational skills, and maximum detection capacity. Most CDCs reported a lack of staff and funds for personnel, which should be a priority in China's upcoming public health reform. The development of sequencing technologies has received considerable attention in CDCs. These are mainly used to study respiratory viruses such as influenza and SARS-CoV-2. The COVID-19 pandemic has driven development of the CDCs in China, and personnel and funds are considered key factors in improving the detection capacity of CDC p-labs.

A Meta-summary and Bioinformatic Analysis Identified Interleukin 6 as a Master Regulator of COVID-19 Severity Biomarkers

With the rising demand for improved COVID-19 disease monitoring and prognostic markers, studies have aimed to identify biomarkers using a range of screening methods. However, the selection of biomarkers for validation from large datasets may result in potentially important biomarkers being overlooked when datasets are considered in isolation. Here, we have utilized a meta-summary approach to investigate COVID-19 biomarker datasets to identify conserved biomarkers of COVID-19 severity. This approach identified a panel of 17 proteins that showed a consistent direction of change across two or more datasets. Furthermore, bioinformatics analysis of these proteins highlighted a range of enriched biological processes that include inflammatory responses and compromised integrity of physiological systems including cardiovascular, neurological, and metabolic. A panel of upstream regulators of the COVID-19 severity biomarkers were identified, including chemical compounds currently under investigation for COVID-19 treatment. One of the upstream regulators, interleukin 6 (IL6), was identified as a “master regulator” of the severity biomarkers. COVID-19 disease severity is intensified due to the extreme viral immunological reaction that results in increased inflammatory biomarkers and cytokine storm. Since IL6 is the primary stimulator of cytokines, it could be used independently as a biomarker in determining COVID-19 disease progression, in addition to a potential therapeutic approach targeting IL6. The array of upstream regulators of the severity biomarkers identified here serve as attractive candidates for the development of new therapeutic approaches to treating COVID-19. In addition, the findings from this study highlight COVID-19 severity biomarkers which represent promising, robust biomarkers for future validation studies for their use in defining and monitoring disease severity and patient prognosis.

Cell tropism and viral clearance during SARS-CoV-2 lung infection

Pulmonary capillary microthrombosis has been proposed as a major pathogenetic factor driving severe COVID-19. Autopsy studies reported endothelialitis but it is under debate if it is caused by SARS-CoV-2 infection of endothelial cells. In this study, RNA in situ hybridization was used to detect viral RNA and to identify the infected cell types in lung tissue of 40 patients with fatal COVID-19. SARS-CoV-2 Spike protein-coding RNA showed a steadily decreasing signal abundance over a period of three weeks. Besides the original virus strain the variants of concern Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529) could also be detected by the assay. Viral RNA was mainly detected in alveolar macrophages and pulmonary epithelial cells, while only single virus-positive endothelial cells were observed even in cases with high viral load suggesting that viral infection of endothelial cells is not a key factor for the development of pulmonary capillary microthrombosis.

Estimation of timing of infection from longitudinal SARS-CoV-2 viral load data: mathematical modelling study

Background

Multiple waves of the COVID-19 epidemic have hit most countries by the end of 2021. Most of those waves are caused by emergence and importation of new variants. To prevent importation of new variants, combination of border control and contact tracing is essential. However, the timing of infection inferred by interview is influenced by recall bias and hinders the contact tracing process.

Methods

We propose a novel approach to infer the timing of infection, by employing a within-host model to capture viral load dynamics after the onset of symptoms. We applied this approach to ascertain secondary transmission which can trigger outbreaks. As a demonstration, the 12 initial reported cases in Singapore, which were considered as imported because of their recent travel history to Wuhan, were analyzed to assess whether they are truly imported.

Results

Our approach suggested that 6 cases were infected prior to the arrival in Singapore, whereas other 6 cases might have been secondary local infection. Three among the 6 potential secondary transmission cases revealed that they had contact history to previously confirmed cases.

Conclusions

Contact trace combined with our approach using viral load data could be the key to mitigate the risk of importation of new variants by identifying cases as early as possible and inferring the timing of infection with high accuracy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07646-2.

Diagnostic accuracy of CRISPR technology for detecting SARS-CoV-2: a systematic review and meta-analysis

OBJECTIVE

To evaluate the diagnostic accuracy of CRISPR-Cas technology for SARS-CoV-2.

METHODS

In our study, RT-qPCR is defined as the reference standard. Data was collected independently and assessed by Quality Assessment of Diagnostic Accuracy Studies (QUADAS)-2 tool. A bivariate model for pooling was employed to estimates of sensitivity and specificity and subgroups analysis was used to explore heterogeneity.

RESULTS

2264 samples and 6 countries from 28 articles were extracted for evaluating the accuracy of CRISPR technology for diagnosing SARS-CoV-2. The overall pooled sensitivity and specificity of CRISPR technology were 0.98 (95% CI: 0.95-0.99) and 1.0 (95% CI: 0.98-1.00), respectively. As for literature quality assessment, high risks in patient selection bias and unclear risk of index test bias may affect accuracy. Subgroup analysis draws significant conclusions. CRISPR-Cas12 is more applicable for molecular diagnostics for its active editing characteristics. RT-LAMP and RT-RPA are usually used for pre-amplification and combined with fluorescence detection to output results quantitatively. Nasopharyngeal swabs and dual-genes perform greatly in our study.

CONCLUSION

The results concluded from all studies showed that CRISPR technology is a promising and accurate molecular method for detecting SARS-CoV-2. Standard methods including comparable sample material, patient selection, operating procedure and operators should be established.

A new droplet digital PCR assay: improving detection of paucibacillary smear-negative pulmonary tuberculosis

BACKGROUND

Smear-negative pulmonary tuberculosis (PTB) is difficult to diagnose. Current diagnosis and treatment monitoring methods have inherent limitations. Droplet digital PCR (ddPCR) is a new technique with high sensitivity. This study presents a novel ddPCR for rapid and sensitive identification of Mycobacterium tuberculosis (MTB).

METHODS

MTB DNA was detected in respiratory specimens from suspected PTB cases using ddPCR assay, which was directed at two different locations within IS6110. We, for the first time, evaluated the clinical diagnostic ability of this ddPCR for paucibacillary smear-negative PTB.

RESULTS

A total of 605 PTB suspects were recruited, including 263 confirmed PTB patients (84.03% from smear-negative PTB) and 342 non-PTB. The sensitivity and specificity of IS6110 ddPCR were 61.22% (95% confidence interval (CI), 55.00%-67.10%) and 95.03% (95% CI, 92.20%-97.10%) for total PTB, and 57.92% (95% CI, 51.10%-64.50%) and 94.57% (95% CI, 91.20%-96.90%) for smear-negative PTB. ddPCR assay outperformed Xpert MTB/RIF (53.08% vs. 28.46%, p = 0.020) in smear-negative PTB detection. Furthermore, effective anti-tuberculosis treatment was linked to significantly lower IS6110 copies detected by ddPCR.

CONCLUSIONS

Herein, we developed and validated a highly sensitive and robust ddPCR assay for MTB quantification in respiratory specimens, which improve diagnosis and therapeutic effect evaluation of smear-negative PTB.

Assessment of Clinical Profile and Treatment Outcome in Vaccinated and Unvaccinated SARS-CoV-2 Infected Patients

Vaccines against severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) infection, which causes coronavirus disease–19 (COVID-19) in humans, have been developed and are being tested for safety and efficacy. We conducted the cross-sectional prospective cohort study on 820 patients who were positive for SARS-CoV-2 and were admitted to Princess Krishnajammanni trauma care centre (PKTCC), Mysore, which was converted to a designated COVID hospital between April 2021 to July 2021. After obtaining the informed consent, RT-PCR report, vaccination certificate and patient history, patients were classified according to their vaccination status. Results from the study showed decreases in serum ferritin levels, clinical symptoms, improvement in oxygen saturation, early recovery in patients having diabetes and hypertension, and a substantial reduction in the overall duration of hospital stay in vaccinated patients compared to unvaccinated patients. Further, fully vaccinated patients showed better outcomes compared to single dose vaccinated and nonvaccinated patients. Taken together, our findings reaffirm the vaccine’s effectiveness in reducing case fatality and promoting faster recovery compared to nonvaccinated patients. Efforts to increase the number of immunized subjects in the community help to achieve herd immunity and offer protection against the severity of COVID-19 and associated complications while minimizing the public health and economic burden.

An external quality assessment for the molecular testing of the SARS-CoV-2 virus genome in Zhejiang Province, China

The COVID-19 pandemic has necessitated the rapid expansion of laboratories that conduct SARS-CoV-2 tests. A provincial external quality assessment (EQA) scheme on SARS-CoV-2 tests was organized by Zhejiang Provincial CDC to assess the accuracy of the tests in individual CDC municipal and county laboratories in Zhejiang Province, China. Three positive samples in high, medium, and low concentrations, respectively, were prepared using the serial dilutions from the culture with the viral titer concentration of 1×10^6.3 TCID50/mL, and one negative sample were included. A total of 93 laboratories participated, contributing results from 36 distinct combinations of nucleic acid extraction methods and PCR reagents. There was 100% concordance among all laboratories for all EQA samples, and no false-positive or false-negative results were observed. The EQA survey provides confidence in the identification of infected individuals or asymptomatic populations and assurance for clinical and public health decision-making based on test results.

Elevated SARS-CoV-2 in peripheral blood and increased COVID-19 severity in American Indians/Alaska Natives

Epidemiological data across the United States show health disparities in COVID-19 infection, hospitalization, and mortality by race/ethnicity. While the association between elevated SARS-CoV-2 viral loads (VLs) (i.e. upper respiratory tract (URT) and peripheral blood (PB)) and increased COVID-19 severity has been reported, data remain largely unavailable for some disproportionately impacted racial/ethnic groups, particularly for American Indian or Alaska Native (AI/AN) populations. As such, we determined the relationship between SARS-CoV-2 VL dynamics and disease severity in a diverse cohort of hospitalized patients. Results presented here are for study participants (n = 94, ages 21-88 years) enrolled in a prospective observational study between May and October 2020 who had SARS-CoV-2 viral clades 20A, C, and G. Based on self-reported race/ethnicity and sample size distribution, the cohort was stratified into two groups: (AI/AN, n = 43) and all other races/ethnicities combined (non-AI/AN, n = 51). SARS-CoV-2 VLs were quantified in the URT and PB on days 0-3, 6, 9, and 14. The strongest predictor of severe COVID-19 in the study population was the mean VL in PB (OR = 3.34; P = 2.00 × 10-4). The AI/AN group had the following: (1) comparable co-morbidities and admission laboratory values, yet more severe COVID-19 (OR = 4.81; P = 0.014); (2) a 2.1 longer duration of hospital stay (P = 0.023); and (3) higher initial and cumulative PB VLs during severe disease (P = 0.025). Moreover, self-reported race/ethnicity as AI/AN was the strongest predictor of elevated PB VLs (β = 1.08; P = 6.00 × 10-4) and detection of SARS-CoV-2 in PB (hazard ratio = 3.58; P = 0.004). The findings presented here suggest a strong relationship between PB VL (magnitude and frequency) and severe COVID-19, particularly for the AI/AN group.

The COVID-19 infection control response at a large stand-alone comprehensive cancer center in Los Angeles County

BACKGROUND

The City of Hope National Medical Center (COH) is the only stand-alone comprehensive cancer center in Los Angeles, a county that was deemed a COVID-19 pandemic epicenter at the height of the 2020 winter surge. The immunocompromised patient population frequently experienced delays in infection control guidelines from local and government bodies due to minimal data available in comparison to the general population. This required COH to make swift, informed decisions for the best interest of the patient population.

AIM

Here, we review the comprehensive COVID-19 infection control response conducted at COH within the context of a high-risk patient population, predominately comprised of patients with hematologic malignancies.

METHODS AND RESULTS

This infection control response focused on prevention of COVID-19 transmission on campus, COVID-19 testing, and isolation management. These efforts consisted of COVID-19 screening, limitation of personnel on campus, source control, contact tracing, COVID-19 vaccination, establishment of in-house testing and implementation and management of COVID-19 testing. Between January 2020 and September 2021, COH implemented a robust in-house testing program, completed well over 1000 contact traces, ensured COVID-19 vaccinations were distributed to all eligible staff and patients, and established an algorithm for COVID-19 infection resolution, all without compromising the number of hematopoietic stem cell transplants (HCTs) performed, surgical volume, or healthcare-associated standardized infection ratios (SIR).

CONCLUSION

Institutional collaboration and attention to infection control was pivotal to minimizing the burden of the COVID-19 pandemic.

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.

A reverse-transcription droplet digital PCR assay to detect and quantify SARS-CoV-2 RNA in upper respiratory tract specimens

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Symptoms are variable and range from asymptomatic or mild to severe (i.e., pneumonia) in both healthy and immunocompromised patients. We developed a reverse-transcription droplet digital PCR (RT-ddPCR) assay for quantification of SARS-CoV-2 RNA in clinical nasopharyngeal and oropharyngeal swab specimens and evaluated the assay, including reproducibility, agreement of results, analytical measurement range, linearity, analytical sensitivity, and analytical specificity. This quantitative assay had a LoD of 218 copies/mL of viral transport media, with a linear quantification range from 500 to 5,000,000 copies/mL (R² of 0.9817 and 0.9853 for N1 and N2 targets, respectively). Qualitative agreement of categorical results was 90.5% (57/63) between the reference and RT-ddPCR assays. Quantitative agreement between the two assays showed correlation, with R² of 0.9726 and 0.9713 for N1 and N2 targets, respectively. No cross-reactivity with common coronavirus strains was detected. This SARS-CoV-2 quantitative RT-ddPCR assay may be a useful tool for a variety of applications including identification of patients with low viral load and serial monitoring of viral load in respiratory tracts specimens of patients for evaluation of the efficacy of therapy for COVID-19.

Micro/nano biomedical devices for point-of-care diagnosis of infectious respiratory diseases

Corona Virus Disease 2019 (COVID-19) has developed into a global pandemic in the last two years, causing significant impacts on our daily life in many countries. Rapid and accurate detection of COVID-19 is of great importance to both treatments and pandemic management. Till now, a variety of point-of-care testing (POCT) approaches devices, including nucleic acid-based test and immunological detection, have been developed and some of them has been rapidly ruled out for clinical diagnosis of COVID-19 due to the requirement of mass testing. In this review, we provide a summary and commentary on the methods and biomedical devices innovated or renovated for the quick and early diagnosis of COVID-19. In particular, some of micro and nano devices with miniaturized structures, showing outstanding analytical performances such as ultra-sensitivity, rapidness, accuracy and low cost, are discussed in this paper. We also provide our insights on the further implementation of biomedical devices using advanced micro and nano technologies to meet the demand of point-of-care diagnosis and home testing to facilitate pandemic management. In general, our paper provides a comprehensive overview of the latest advances on the POCT device for diagnosis of COVID-19, which may provide insightful knowledge for researcher to further develop novel diagnostic technologies for rapid and on-site detection of pathogens including SARS-CoV-2.

The pathogenesis of neurologic symptoms of the postacute sequelae of severe acute respiratory syndrome coronavirus 2 infection

PURPOSE OF REVIEW

The coronavirus disease 2019 (COVID) pandemic has resulted in significant mortality and morbidity globally. Patients who survive infection may develop continuing disease collectively known as the postacute sequelae of severe acute respiratory syndrome coronavirus 2 infection (PASC), which includes neurologic symptoms especially fatigue and cognitive impairment. The pathogenic mechanisms driving PASC are unknown although a postinfectious process, persistent infection, or lasting pathophysiological changes that occur during acute infection are all suspected to contribute.

RECENT FINDINGS

Here we review the current evidence underlying potential pathogenic mechanisms of the neurological complications of PASC with particular emphasis on the evidence for postinfectious immune processes and viral persistence.

SUMMARY

Immune dysregulation favoring persistent inflammation, including neuroinflammation and enhanced autoimmunity, are present in patients with COVID and likely contribute to the development of PASC. Limited evidence of viral persistence exists but may explain the ongoing inflammatory processes and affinity maturation observed in some patients recovering from COVID infections. No specific studies to date have tied persistent infection to PASC. CNS trauma, in particular hypoxic changes in the CNS, and psychiatric complications occur with greater frequency in patients with COVID and may contribute to the development of PASC. Future research is needed to fully understand the pathophysiological mechanisms driving PASC.

A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus

BACKGROUND

Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions.

METHODS

The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing.

RESULTS

The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 10³ pfu/ml (Ct, 22.4) for whole genome assembly and 10¹ pfu/ml (Ct, 30) for metagenomics detection.

CONCLUSIONS

The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.

Prevention and Treatment of Life-Threatening COVID-19 May Be Possible with Oxygen Treatment

Most SARS CoV-2 infections probably occur unnoticed or cause only cause a mild common cold that does not require medical intervention. A significant proportion of more severe cases is characterized by early neurological symptoms such as headache, fatigue, and impaired consciousness, including respiratory distress. These symptoms suggest hypoxia, specifically affecting the brain. The condition is best explained by primary replication of the virus in the nasal respiratory and/or the olfactory epithelia, followed by an invasion of the virus into the central nervous system, including the respiratory centers, either along a transneural route, through disruption of the blood-brain barrier, or both. In patients, presenting with early dyspnea, the primary goal of therapy should be the reversal of brain hypoxia as efficiently as possible. The first approach should be intermittent treatment with 100% oxygen using a tight oronasal mask or a hood. If this does not help within a few hours, an enclosure is needed to increase the ambient pressure. This management approach is well established in the hypoxia-related diseases in diving and aerospace medicine and preserves the patient’s spontaneous breathing. Preliminary research evidence indicates that even a small elevation of the ambient pressure might be lifesaving. Other neurological symptoms, presenting particularly in long COVID-19, suggest imbalance of the autonomous nervous system, i.e., dysautonomia. These patients could benefit from vagal nerve stimulation.

Clinical Validation of a Rapid Variant-Proof RT-RPA Assay for the Detection of SARS-CoV-2

The COVID-19 pandemic has unveiled a pressing need to expand the diagnostic landscape to permit high-volume testing in peak demand. Rapid nucleic acid testing based on isothermal amplification is a viable alternative to real-time reverse transcription polymerase chain reaction (RT-PCR) and can help close this gap. With the emergence of SARS-CoV-2 variants of concern, clinical validation of rapid molecular tests needs to demonstrate their ability to detect known variants, an essential requirement for a robust pan-SARS-CoV-2 assay. To date, there has been no clinical validation of reverse transcription recombinase polymerase amplification (RT-RPA) assays for SARS-CoV-2 variants. We performed a clinical validation of a one-pot multi-gene RT-RPA assay with the E and RdRP genes of SARS-CoV-2 as targets. The assay was validated with 91 nasopharyngeal samples, with a full range of viral loads, collected at University College London Hospitals. Moreover, the assay was tested with previously sequenced clinical samples, including eleven lineages of SARS-CoV-2. The rapid (20 min) RT-RPA assay showed high sensitivity and specificity, equal to 96% and 97%, respectively, compared to gold standard real-time RT-PCR. The assay did not show cross-reactivity with the panel of respiratory pathogens tested. We also report on a semi-quantitative analysis of the RT-RPA results with correlation to viral load equivalents. Furthermore, the assay could detect all eleven SARS-CoV-2 lineages tested, including four variants of concern (Alpha, Beta, Delta, and Omicron). This variant-proof SARS-CoV-2 assay offers a significantly faster and simpler alternative to RT-PCR, delivering sensitive and specific results with clinical samples.

Sponge Whirl-Pak Sampling Method and Droplet Digital RT-PCR Assay for Monitoring of SARS-CoV-2 on Surfaces in Public and Working Environments

The SARS-CoV-2 can spread directly via saliva, respiratory aerosols and droplets, and indirectly by contact through contaminated objects and/or surfaces and by air. In the context of COVID-19 fomites can be an important vehicle of virus transmission and contribute to infection risk in public environments. The aim of the study was to analyze through surface sampling (sponge method) the presence of SARS-CoV-2 in public and working environments, in order to evaluate the risk for virus transmission. Seventy-seven environmental samples were taken using sterile sponges in 17 animal farms, 4 public transport buses, 1 supermarket and 1 hotel receptive structure. Furthermore, 246 and 93 swab samples were taken in the farms from animals and from workers, respectively. SARS-CoV-2 detection was conducted by real-time RT-PCR and by digital droplet RT-PCR (dd RT-PCR) using RdRp, gene E and gene N as targets. None of the human and animal swab samples were positive for SARS-CoV-2, while detection was achieved in 20 of the 77 sponge samples (26%) using dd RT-PCR. Traces of the RdRp gene, gene E and gene N were found in 17/77 samples (22%, average concentration 31.2 g.c./cm², range 5.6 to 132 g.c./cm²), 8/77 samples (10%, average concentration 15.1 g.c./cm², range 6 to 36 g.c./cm²), and in 1/77 (1%, concentration 7.2 g.c./cm²). Higher detection rates were associated with sampling in animal farms and on public transport buses (32% and 30%) compared to the supermarket (21%) and the hotel (no detection). The result of the study suggests that the risk of contamination of surfaces with SARS-CoV-2 increases in environments in which sanitation strategies are not suitable and/or in highly frequented locations, such as public transportation. Considering the analytical methods, the dd RT-PCR was the only approach achieving detection of SARS-CoV-2 traces in environmental samples. Thus, dd RT-PCR emerges as a reliable tool for sensitive SARS-CoV-2 detection.

Persistent viral RNA shedding of SARS-CoV-2 is associated with delirium incidence and six-month mortality in hospitalized COVID-19 patients

BACKGROUND

Persistent viral RNA shedding of SARS-CoV-2 following COVID-19 has increasingly been recognized, with limited understanding of its implications on outcomes in hospitalized COVID-19 patients.

METHODS

We retrospectively assessed for persistent viral shedding across Northwestern Medicine Healthcare (NMHC) patients between March and August 2020. We assessed for predictors of persistent viral shedding, in-hospital delirium, and six-month mortality using binary logistic regression.

RESULTS

Of the 2,518 hospitalized patients with an RT-PCR-confirmed diagnosis of COVID-19, 959 underwent repeat SARS-CoV-2 RT-PCR at least fourteen days from initial positive testing. Of those, 405 (42.2%) patients were found to have persistent viral shedding. Persistent viral shedding was associated with male sex, increased BMI, diabetes mellitus, chronic kidney disease, and exposure to corticosteroids during initial COVID-19 hospitalization. Persistent viral shedding was independently associated with incidence of in-hospital delirium after adjusting for factors including severity of respiratory dysfunction (OR 2.45; 95% CI 1.75, 3.45). Even after adjusting for age, severity of respiratory dysfunction, and occurrence of in-hospital delirium, persistent viral shedding remained significantly associated with increased six-month mortality (OR 2.43; 95% CI 1.42, 4.29).

CONCLUSIONS

Persistent viral shedding occurs frequently in hospitalized COVID-19 patients and is associated with in-hospital delirium and increased six-month mortality.

A Randomized, Double-Blind, Placebo-Controlled, Multicenter Study to Evaluate the Safety and Efficacy of ThymoQuinone Formula (TQF) for Treating Outpatient SARS-CoV-2

There is an urgent need for an oral drug for the treatment of mild to moderate outpatient SARS-CoV-2. Our preclinical and clinical study’s aim was to determine the safety and preliminary efficacy of oral TQ Formula (TQF), in the treatment of outpatient SARS-CoV-2. In a double-blind, placebo-controlled phase 2 trial, we randomly assigned (1:1 ratio) non-hospitalized, adult (>18 years), symptomatic SARS-CoV-2 patients to receive oral TQF or placebo. The primary endpoints were safety and the median time-to-sustained-clinical-response (SCR). SCR was 6 days in the TQF arm vs. 8 days in the placebo arm (p = 0.77), and 5 days in the TQF arm vs. 7.5 days in the placebo arm in the high-risk cohort, HR 1.55 (95% CI: 0.70, 3.43, p = 0.25). No significant difference was found in the rate of AEs (p = 0.16). TQF led to a significantly faster decline in the total symptom burden (TSB) (p < 0.001), and a significant increase in cytotoxic CD8+ (p = 0.042) and helper CD4+ (p = 0.042) central memory T lymphocytes. TQF exhibited an in vitro inhibitory effect on the entry of five SARS-CoV-2 variants. TQF was well-tolerated. While the median time-to-SCR did not reach statistical significance; it was shorter in the TQF arm and preclinical/clinical signals of TQF activity across multiple endpoints were significant. Therefore, a confirmatory study is planned.

Ocular surface disturbance in patients after acute COVID-19

Background

We investigated the ocular surface disturbances in COVID‐19 patients discharged from the hospital.

Methods

One hundred and seventy‐nine eyes of 109 healthy participants and 456 eyes of 228 post‐COVID‐19 patients received comprehensive eye examinations; the latter were interviewed with questionnaires on ocular symptoms before and after COVID‐19 diagnosis. Associations of ocular surface manifestations with virological and ophthalmic parameters were evaluated by multivariable mixed linear or logistic regression models.

Results

Mean interval between COVID‐19 diagnosis and ophthalmic evaluation was 52.23 ± 16.12 days. The severity of meibomian gland dysfunction (MGD) based on clinical staging was higher in post‐COVID‐19 than healthy eyes (1.14 ± 0.67 vs. 0.92 ± 0.68, p = 0.002) and so was ocular surface staining score (0.60 ± 0.69 vs. 0.49 ± 0.68, p = 0.044). Patients requiring supplementary oxygen during hospitalisation had shorter tear break‐up time (β −1.63, 95% CI ‐2.61 to −0.65). Cycle threshold (Ct) value from upper respiratory samples (inversely correlated with viral load) at diagnosis had an OR = 0.91 (95% CI 0.84–0.98) with new ocular surface symptoms 4 weeks after diagnosis. The presence of ocular surface symptoms 1 week prior to COVID‐19 diagnosis showed an OR of 20.89 (95% CI 6.35–68.66) of persistent or new ocular symptoms 4 weeks afterward.

Conclusions

MGD and ocular surface staining are more common and severe in post‐COVID‐19 patients. Patients with higher viral loads have greater risks of ocular surface symptoms. Patients requiring supplementary oxygen are more likely to show tear film instability. Ocular surface evaluation should be considered 1–3 months following hospital discharge for any COVID‐19 patient.

Rapid and Accurate Detection of SARS Coronavirus 2 by Nanopore Amplicon Sequencing

Objective

We aimed to evaluate the performance of nanopore amplicon sequencing detection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples.

Method

We carried out a single-center, prospective cohort study in a Wuhan hospital and collected a total of 86 clinical samples, including 54 pharyngeal swabs, 31 sputum samples, and 1 fecal sample, from 86 patients with coronavirus disease 2019 (COVID-19) from Feb 20 to May 15, 2020. We performed parallel detection with nanopore-based genome amplification and sequencing (NAS) on the Oxford Nanopore Technologies (ONT) minION platform and routine reverse transcription quantitative polymerase chain reaction (RT-qPCR). In addition, 27 negative control samples were detected using the two methods. The sensitivity and specificity of NAS were evaluated and compared with those of RT-qPCR.

Results

The viral read number and reference genome coverage were both significantly different between the two groups of samples, and the latter was a better indicator for SARS-CoV-2 detection. Based on the reference genome coverage, NAS revealed both high sensitivity (96.5%) and specificity (100%) compared with RT-qPCR (80.2 and 96.3%, respectively), although the samples had been stored for half a year before the detection. The total time cost was less than 15 h, which was acceptable compared with that of RT-qPCR (∼2.5 h). In addition, the reference genome coverage of the viral reads was in line with the cycle threshold value of RT-qPCR, indicating that this number could also be used as an indicator of the viral load in a sample. The viral load in sputum might be related to the severity of the infection, particularly in patients within 4 weeks after onset of clinical manifestations, which could be used to evaluate the infection.

Conclusion

Our results showed the high sensitivity and specificity of the NAS method for SARS-CoV-2 detection compared with RT-qPCR. The sequencing results were also used as an indicator of the viral load to display the viral dynamics during infection. This study proved the wide application prospect of nanopore sequencing detection for SARS-CoV-2 and may more knowledge about the clinical characteristics of COVID-19.

Sensitive Detection of SARS-CoV-2 Using a Novel Plasmonic Fiber Optic Biosensor Design

The coronavirus (COVID-19) pandemic has put the entire world at risk and caused an economic downturn in most countries. This work provided theoretical insight into a novel fiber optic-based plasmonic biosensor that can be used for sensitive detection of SARS-CoV-2. The aim was always to achieve reliable, sensitive, and reproducible detection. The proposed configuration is based on Ag-Au alloy nanoparticle films covered with a layer of graphene which promotes the molecular adsorption and a thiol-tethered DNA layer as a ligand. Here, the combination of two recent approaches in a single configuration is very promising and can only lead to considerable improvement. We have theoretically analyzed the sensor performance in terms of sensitivity and resolution. To highlight the importance of the new configuration, a comparison was made with two other sensors. One is based on gold nanoparticles incorporated into a host medium; the other is composed of a bimetallic Ag-Au layer in the massive state. The numerical results obtained have been validated and show that the proposed configuration offers better sensitivity (7100 nm\RIU) and good resolution (figure of merit; FOM = 38.88 RIU - 1 and signal-to-noise ratio; SNR = 0.388). In addition, a parametric study was performed such as the graphene layers' number and the size of the nanoparticles.

Exploring Longitudinal Cough, Breath, and Voice Data for COVID-19 Disease Progression Prediction via Sequential Deep Learning: Model Development and Validation

Background

Recent work has shown the potential of using audio data (eg, cough, breathing, and voice) in the screening for COVID-19. However, these approaches only focus on one-off detection and detect the infection, given the current audio sample, but do not monitor disease progression in COVID-19. Limited exploration has been put forward to continuously monitor COVID-19 progression, especially recovery, through longitudinal audio data. Tracking disease progression characteristics and patterns of recovery could bring insights and lead to more timely treatment or treatment adjustment, as well as better resource management in health care systems.

Objective

The primary objective of this study is to explore the potential of longitudinal audio samples over time for COVID-19 progression prediction and, especially, recovery trend prediction using sequential deep learning techniques.

Methods

Crowdsourced respiratory audio data, including breathing, cough, and voice samples, from 212 individuals over 5-385 days were analyzed, alongside their self-reported COVID-19 test results. We developed and validated a deep learning–enabled tracking tool using gated recurrent units (GRUs) to detect COVID-19 progression by exploring the audio dynamics of the individuals’ historical audio biomarkers. The investigation comprised 2 parts: (1) COVID-19 detection in terms of positive and negative (healthy) tests using sequential audio signals, which was primarily assessed in terms of the area under the receiver operating characteristic curve (AUROC), sensitivity, and specificity, with 95% CIs, and (2) longitudinal disease progression prediction over time in terms of probability of positive tests, which was evaluated using the correlation between the predicted probability trajectory and self-reported labels.

Results

We first explored the benefits of capturing longitudinal dynamics of audio biomarkers for COVID-19 detection. The strong performance, yielding an AUROC of 0.79, a sensitivity of 0.75, and a specificity of 0.71 supported the effectiveness of the approach compared to methods that do not leverage longitudinal dynamics. We further examined the predicted disease progression trajectory, which displayed high consistency with longitudinal test results with a correlation of 0.75 in the test cohort and 0.86 in a subset of the test cohort with 12 (57.1%) of 21 COVID-19–positive participants who reported disease recovery. Our findings suggest that monitoring COVID-19 evolution via longitudinal audio data has potential in the tracking of individuals’ disease progression and recovery.

Conclusions

An audio-based COVID-19 progression monitoring system was developed using deep learning techniques, with strong performance showing high consistency between the predicted trajectory and the test results over time, especially for recovery trend predictions. This has good potential in the postpeak and postpandemic era that can help guide medical treatment and optimize hospital resource allocations. The changes in longitudinal audio samples, referred to as audio dynamics, are associated with COVID-19 progression; thus, modeling the audio dynamics can potentially capture the underlying disease progression process and further aid COVID-19 progression prediction. This framework provides a flexible, affordable, and timely tool for COVID-19 tracking, and more importantly, it also provides a proof of concept of how telemonitoring could be applicable to respiratory diseases monitoring, in general.

RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants

With the rapid emergence and spread of SARS-CoV-2 variants, development of vaccines with broad and potent protectivity has become a global priority. Here, we designed a lipid nanoparticle-encapsulated, nucleoside-unmodified mRNA (mRNA-LNP) vaccine encoding the trimerized receptor-binding domain (RBD trimer) and showed its robust capability in inducing broad and protective immune responses against wild-type and major variants of concern (VOCs) in the mouse model of SARS-CoV-2 infection. The protectivity was correlated with RBD-specific B cell responses especially the long-lived plasma B cells in bone marrow, strong ability in triggering BCR clustering, and downstream signaling. Monoclonal antibodies isolated from vaccinated animals demonstrated broad and potent neutralizing activity against VOCs tested. Structure analysis of one representative antibody identified a novel epitope with a high degree of conservation among different variants. Collectively, these results demonstrate that the RBD trimer mRNA vaccine serves as a promising vaccine candidate against SARS-CoV-2 variants and beyond.

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A mRNA vaccine encoding the RBD trimer of wild-type SARS-CoV-2 was designed and studied

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The vaccine elicited strong RBD-specific memory and plasma B cell responses

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The vaccine induced broadly serum and monoclonal neutralizing antibodies in mice

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The vaccine induced strong and protective immunity against major SARS-CoV-2 variants

Performance of the LumiraDx Microfluidic Immunofluorescence Point-of-Care SARS-CoV-2 Antigen Test in Asymptomatic Adults and Children

OBJECTIVES

The LumiraDx SARS-CoV-2 Ag Test has previously been shown to accurately detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals symptomatic for coronavirus disease 2019 (COVID-19). This evaluation investigated the LumiraDx SARS-CoV-2 Ag Test as an aid in the diagnosis of SARS-CoV-2 infection in asymptomatic adults and children.

METHODS

Asymptomatic individuals at high risk of COVID-19 infection were recruited in 5 point-of-care (POC) settings. Two paired anterior nasal swabs were collected from each participant, tested by using the LumiraDx SARS-CoV-2 Ag Test at the POC, and compared with results from reverse transcription-polymerase chain reaction (RT-PCR) assays (cobas 6800 [Roche Diagnostics] or TaqPath [Thermo Fisher Scientific]). We calculated positive percent agreement (PPA) and negative percent agreement (NPA), then stratified results on the basis of RT-PCR reference platform and cycle threshold.

RESULTS

Of the 222 included study participants confirmed to be symptom-free for at least 2 weeks before testing, the PPA was 82.1% (95% confidence interval [CI], 64.4%-92.1%). The LumiraDx SARS-CoV-2 Ag Test correctly identified 95.8% (95% CI, 79.8%-99.3%) of the samples confirmed positive in fewer than 33 RT-PCR cycles and 100% (95% CI, 85.1%-100%) in fewer than 30 RT-PCR cycles while maintaining 100% NPA.

CONCLUSIONS

This rapid, high-sensitivity test can be used to screen asymptomatic patients for acute SARS-CoV-2 infection in clinic- and community-based settings.

Interleukin-6-Production Is Responsible for Induction of Hepatic Synthesis of Several Chemokines as Acute-Phase Mediators in Two Animal Models: Possible Significance for Interpretation of Laboratory Changes in Severely Ill Patients

Simple Summary

The release of acute-phase proteins and cytokine storms are considered critical parameters for the progression of COVID-19 disease. The increase in the serum levels of cytokines such as IL6 and IL8 observed in patients primarily infected with the SARS-CoV-2 virus has been used to determine the severity of clinical conditions resulting from infection and for prognostic purposes. Animal models have been used to understand the mechanisms of the changes in homeostasis observed under pathological conditions. In the present study, we therefore report the changes in serum levels and hepatic gene expression of cytokines and chemokines in two different animal models of acute-phase responses. The acute-phase response is a transient emergency response aimed at preserving life and bringing about the changes necessary to reduce and repair tissue damage after the removal of damaging noxious agents. Our data suggest that the liver may be responsible for the increase in the serum levels of cytokines and chemokines as part of the body’s defense response to tissue damage. It is therefore doubtful that inhibiting this response at any stage after infection could improve the prognosis of patients. These results may help to interpret the laboratory changes observed in critically ill patients, as may be the case following SARS-CoV-2 infection.

Abstract

A mild to moderate increase in acute-phase proteins (APPs) and a decrease in serum albumin levels are detected in hospitalized COVID-19 patients. A similar trend is also observed for acute-phase cytokines (APC), mainly IL6, besides chemokines (e.g., CXCL8 and CCL2). However, the source of the chemokines in these patients at different stages of disease remains to be elucidated. We investigated hepatic gene expression of CXC- and CC-chemokines in a model of a localized extrahepatic aseptic abscess and in a model of septicemia produced by the intramuscular injection of turpentine oil (TO) into each hindlimb or lipopolysaccharide (LPS) intraperitoneally (i.p.) in rats and mice (wild-type (WT) and IL6-KO). Together with a striking increase in the serum IL6 level, strong serum CXCL2 and CXCL8 concentrations were detected. Correspondingly, rapid (2 h) upregulation of CXCL1, CXCL2, CXCL5, and CXCL8 was observed in rat liver after intramuscular TO injection. The induction of the gene expression of CXCL1 and CXCL8 was the fastest and strongest. The hepatic CXC-chemokines behaved like positive APPs that depend on IL6 production by activated macrophages recruited to extrahepatic damaged tissue. Chemokine upregulation was greatly reduced in IL6-KO mice. However, IL6 was dispensable in the LPS–APR model, as massive induction of hepatic chemokines studied was measured in IL6-KO mice.

Current commercial dPCR platforms: technology and market review

Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.

Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.

Singlet oxygen generation in aerosol jet and on biological surfaces

The paper presents steady-state and time-resolved experiments on photophysical processes associated with photodynamic inactivation of infections provided by nebulization of Radachlorin photosensitizer solution. As models of surfaces subjected to photodynamic inactivation we used glass, plant leaf, mushroom cap peel and superficial fascia of chicken and salmon skin flaps. The oxygen content in the photosensitizer solution was varied by blowing with atmospheric air and with pure oxygen. It was shown that singlet oxygen was generated efficiently in the aerosol jet and that its amount increased noticeably at higher oxygen concentrations. The kinetics of photosensitizer photobleaching on different surfaces were found to be significantly different with characteristic decay times varying from seconds for leaf and glass to minutes for fascial flaps. This observation was attributed to much faster oxygen depletion on rough crumbly surfaces of biological samples due to effective oxidation reactions occurred. The singlet oxygen generation and degradation times, and the relative quantum yield were determined on different surfaces by recording time-resolved phosphorescence at about 1270 nm under normoxic and hyperoxic conditions and analyzed on the basis of the set of master equations. The results obtained provide reference marks for choosing optimal irradiation durations for photodynamic inactivation of pathogenic infectious agents (bacteria, mycobacteria, fungi, viruses) on mucous membranes, including the tracheobronchial tree.

Importance of sample input volume for accurate SARS-CoV-2 qPCR testing

Nucleic acid testing is the most widely used detection method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. Currently, a number of COVID-19 real-time quantitative reverse transcription PCR (qPCR) kits with high sensitivity and specificity are available for SARS-CoV-2 testing. However, these qPCR assays are not always reliable in detecting low viral load samples (Ct-value ≥ 35), resulting in inconclusive or false-negative results. Here, we used a Poisson distribution to illustrate the inconsistent performance of qPCR tests in detecting low viral load samples. From this, we concluded that the false-negative outcomes resulted from the random occurrences of sampling zero target molecules in a single test, and the probability to sample zero target molecules in one test decreased significantly with increasing purified RNA or initial sample input volume. At a given RNA concentration of 0.5 copy/μL, the probability of sampling zero RNA molecules decreased from 36.79% to close to 0.67% after increasing the RNA input volume from 2 to 10 μL. A SARS-CoV-2 qPCR assay with an LOD of 300 copies/mL was used to validate the improved consistency of the qPCR tests. We found that the false-negative qPCR results of clinical COVID-19 samples with a Ct ≥ 35 decreased by 50% after increasing the input of purified RNA from 2 to 10 μL. The consistency, accuracy, and robustness of nucleic acid testing for SARS-CoV-2 samples with low viral loads can be improved by increasing the sample input volume.

A prospective study of the impact of glycaemic status on clinical outcomes and anti-SARS-CoV-2 antibody responses among patients with predominantly non-severe COVID-19

AIMS

We carried out this prospective study of predominantly non-severe COVID-19 patients, to evaluate the influence of glycaemic status on clinical outcomes and neutralising antibody (Nab) responses, potentially relevant to the COVID-19 vaccination programme.

METHODS

We included consecutive adults admitted to Queen Mary Hospital for COVID-19 from July 2020-May 2021. Glycaemic status was defined by admission HbA1c. Clinical deterioration was defined by radiological progression/new oxygen requirement/intensive care requirement/death. COVID-19 survivors had Nab measurements at 1-month, 2-month, 3-month and 6-month post-discharge.

RESULTS

Among 605 patients (96.9% non-severe COVID-19; 325 normoglycaemia, 185 prediabetes, 95 diabetes), 74 (12.2%) had clinical deterioration, more likely with worse glycaemic status and higher HbA1c (p < 0.001). Older age (p < 0.001), higher viral loads (p < 0.001), higher C-reactive protein (CRP) (p < 0.001) and symptomatic presentation (p = 0.008), but not glycaemic status/HbA1c, independently predicted clinical deterioration. Older age (p = 0.001), higher CRP (p = 0.038), elevated lactate dehydrogenase (p = 0.046) and interferon treatment (p = 0.001), but not glycaemic status/HbA1c, independently predicted Nab titres. Rate of Nab titre decline was comparable across glycaemic status.

CONCLUSIONS

COVID-19 patients with worse glycaemic status were more likely to deteriorate clinically, mediated through the association of worse glycaemic status with older age, more severe inflammation and higher viral loads. Importantly, Nab responses did not differ across glycaemic status.

Comparison of reverse-transcription qPCR and droplet digital PCR for the detection of SARS-CoV-2 in clinical specimens of hospitalized patients

Accurate detection of severe acute respiratory syndrome coronavirus 2 is not only necessary for viral load monitoring to optimize treatment in hospitalized coronavirus disease 2019 patients, but also critical for deciding whether the patient could be discharged without any risk of viral shedding. Digital droplet PCR (ddPCR) is more sensitive than reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and is usually considered the superior choice. In the current study, we compared the clinical performance of RT-qPCR and ddPCR using oropharyngeal swab samples from patients hospitalized in the temporary Huoshenshan Hospital, Wuhan, Hubei, China. Results demonstrated that ddPCR was indeed more sensitive than RT-qPCR. Negative results might be caused by poor sampling technique or recovered patients, as the range of viral load in these patients varied significantly. In addition, both methods were highly correlated in terms of their ability to detect all three target genes as well as the ratio of copies of viral genes to that of the IC gene. Furthermore, our results evidenced that both methods detected the N gene more easily than the ORF gene. Taken together, these findings imply that the use of ddPCR, as an alternative to RT-qPCR, is necessary for the accurate diagnosis of hospitalized coronavirus disease 2019 patients.

Viral load and disease severity in COVID-19

The relationship between COVID-19 severity and viral load is unknown. Our objective was to assess the association between viral load and disease severity in COVID-19. In this single center observational study of adults with laboratory confirmed SARS-CoV-2, the first positive in-hospital nasopharyngeal swab was used to calculate the log10 copies/ml [log10 copy number (CN)] of SARS-CoV-2. Four categories based on level of care and modified sequential organ failure assessment score (mSOFA) at time of swab were determined. Median log10CN was compared between different levels of care and mSOFA quartiles. Median log10CN was compared in patients who did and did not receive influenza vaccine, and the correlation between log10CN and D-dimer was examined. We found that of 396 patients, 54.3% were male, and 25% had no major comorbidity. Hospital mortality was 15.7%. Median mSOFA was 2 (IQR 0-3). Median log10CN was 5.5 (IQR 3.3-8.0). Median log10CN was highest in non-intubated ICU patients [6.4 (IQR 4.4-8.1)] and lowest in intubated ICU patients [3.6 (IQR 2.6-6.9)] (p value < 0.01). In adjusted analyses, this difference remained significant [mean difference 1.16 (95% CI 0.18-2.14)]. There was no significant difference in log10CN between other groups in the remaining pairwise comparisons. There was no association between median log10CN and mSOFA in either unadjusted or adjusted analyses or between median log10CN in patients with and without influenza immunization. There was no correlation between log10CN and D-dimer. We conclude, in our cohort, we did not find a clear association between viral load and disease severity in COVID-19 patients. Though viral load was higher in non-intubated ICU patients than in intubated ICU patients there were no other significant differences in viral load by disease severity.