Viral Load Dynamics in Sputum and Nasopharyngeal Swab in Patients with COVID-19

In silico identification of viral loads in cough-generated droplets - Seamless integrated analysis of CFPD-HCD-EWF

BACKGROUND AND OBJECTIVE

Respiratory diseases caused by respiratory viruses have significantly threatened public health worldwide. This study presents a comprehensive approach to predict viral dynamics and the generation of stripped droplets within the mucus layer of the respiratory tract during coughing using a larynx-trachea-bifurcation (LTB) model.

METHODS

This study integrates computational fluid-particle dynamics (CFPD), host-cell dynamics (HCD), and the Eulerian wall film (EWF) model to propose a potential means for seamless integrated analysis. The verified CFPD-HCD coupling model based on a 3D-shell model was used to characterize the severe acute respiratory syndrome, coronavirus 2 (SARS-CoV-2) dynamics in the LTB mucus layer, whereas the EWF model was employed to account for the interfacial fluid to explore the generation mechanism and trace the origin site of droplets exhaled during a coughing event of an infected host.

RESULTS

The results obtained using CFPD delineated the preferential deposition sites for droplets in the laryngeal and tracheal regions. Thus, the analysis of the HCD model showed that the viral load increased rapidly in the laryngeal region during the peak of infection, whereas there was a growth delay in the tracheal region (up to day 8 after infection). After two weeks of infection, the high viral load gradually migrated towards the glottic region. Interestingly, the EWF model demonstrated a high concentration of exhaled droplets originating from the larynx. The coupling technique indicated a concurrent high viral load in the mucus layer and site of origin of the exhaled droplets.

CONCLUSIONS

This interdisciplinary research underscores the seamless analysis from initial exposure to virus-laden droplets, the dynamics of viral infection in the LTB mucus layer, and the re-emission from the coughing activities of an infected host. Our efforts aimed to address the complex challenges at the intersection of viral dynamics and respiratory health, which can contribute to a more detailed understanding and targeted prevention of respiratory diseases.

High baseline frequencies of natural killer cells are associated with asymptomatic SARS-CoV-2 infection

This study tested the hypothesis that high frequencies of natural killer (NK) cells are protective against symptomatic SARS-CoV-2 infection. Samples were utilized from the COVID-19 Health Action Response for Marines study, a prospective, observational study of SARS-CoV-2 infection in which participants were enrolled prior to infection and then serially monitored for development of symptomatic or asymptomatic infection. Frequencies and phenotypes of NK cells (CD3-CD14-CD19-CD56+) were assessed by flow cytometry. Individuals that developed asymptomatic infections were found to have higher pre-infection frequencies of total NK cells compared to symptomatic individuals (10.61% [SD 4.5] vs 8.33% [SD 4.6], p = 0.011). Circulating total NK cells decreased over the course of infection, reaching a nadir at 4 weeks, while immature NK cells increased, a finding confirmed by multidimensional reduction analysis. These results indicate that NK cells likely play a key role in controlling the severity of clinical illness in individuals infected with SARS-CoV-2.

Saline nasal irrigation and gargling in COVID-19: a multidisciplinary review of effects on viral load, mucosal dynamics, and patient outcomes

With unrelenting SARS-CoV-2 variants, additional COVID-19 mitigation strategies are needed. Oral and nasal saline irrigation (SI) is a traditional approach for respiratory infections/diseases. As a multidisciplinary network with expertise/experience with saline, we conducted a narrative review to examine mechanisms of action and clinical outcomes associated with nasal SI, gargling, spray, or nebulization in COVID-19. SI was found to reduce SARS-CoV-2 nasopharyngeal loads and hasten viral clearance. Other mechanisms may involve inhibition of viral replication, bioaerosol reduction, improved mucociliary clearance, modulation of ENaC, and neutrophil responses. Prophylaxis was documented adjunctive to personal protective equipment. COVID-19 patients experienced significant symptom relief, while overall data suggest lower hospitalization risk. We found no harm and hence recommend SI use, as safe, inexpensive, and easy-to-use hygiene measure, complementary to hand washing or mask-wearing. In view of mainly small studies, large well-controlled or surveillance studies can help to further validate the outcomes and to implement its use.

Capabilities of Double-Resonance LPG and SPR Methods for Hypersensitive Detection of SARS-CoV-2 Structural Proteins: A Comparative Study

The danger of the emergence of new viral diseases and their rapid spread demands apparatuses for continuous rapid monitoring in real time. This requires the creation of new bioanalytical methods that overcome the shortcomings of existing ones and are applicable for point-of-care diagnostics. For this purpose, a variety of biosensors have been developed and tested in proof-of-concept studies, but none of them have been introduced for commercial use so far. Given the importance of the problem, in this study, long-period grating (LPG) and surface plasmon resonance (SPR) biosensors, based on antibody detection, were examined, and their capabilities for SARS-CoV-2 structural proteins detection were established. Supersensitive detections of structural proteins in the order of several femtomoles were achieved by the LPG method, while the SPR method demonstrated a sensitivity of about one hundred femtomoles. The studied biosensors are compatible in sensitivity with ELISA and rapid antigen tests but, in contrast, they are quantitative, which makes them applicable for acute SARS-CoV-2 infection detection, especially during the early stages of viral replication.

Comparable detection of nasopharyngeal swabs and induced sputum specimens for viral nucleic acid detection of suspected novel coronavirus (SARS-Cov-2) patients in Fayoum governorate, Egypt

Background

The most commonly utilized samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection using real-time quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) are nasopharyngeal swabs (NPS) and oropharyngeal swabs. However, there are some drawbacks. For SARS-CoV-2 detection, induced sputum might be analyzed and may be equivalent to pharyngeal swabs. This study was done to assess the potential superiority of induced sputum over NPS for SARS-CoV-2 detection. Sixty symptomatic COVID-19 patients who attended Fayoum University Hospitals in Fayoum Governorate, Egypt, were included in this cross-sectional descriptive study. Paired NPS and induced sputum samples were collected from each subject on the third and tenth days after symptoms began for RT-qPCR SARS-COV2 diagnosis.

Results

At day 3, 52 (86.7%) of NPS and 48 (80.00%) of induced sputum specimens had positive RT-qPCR results with a significant statistical difference (P = 0.001). At day 10, 41 induced sputum samples (68.3%) were negative, while 19 (31.7%) were positive. Only three (5.0%) of the 19 positive induced sputum samples tested positive for NPS. NPS samples had a higher viral load than induced sputum samples at day 3 [25 (41.7%) vs. 23 (38.3%)]. At day 10, induced sputum samples had a higher viral load than NPS [9 (15.0%) vs. 6 (10.0%)]. A statistically significant positive correlation between the viral load value of the NPS and the induced sputum sample at day 3 (r = 0.497, p = 0.00) denoting similarity in the results of the two types of samples. By ROC analysis, the highest area under the curve for the overall CT value of the induced sputum was (0.604), with a statistically significant difference (p value = 0.0418).

Conclusion

In the early stages of the disease, induced sputum and NPS tests had comparable results, but NPS yielded more false negative results later in the disease course than an induced sputum sample, which yielded higher sample positivity and viral load than NPS. Furthermore, induced sputum collection is a straightforward, non-invasive, and risk-free method. As a result, induced sputum could be useful for COVID-19 confirmation in patients with radiologically or epidemiologically suspected COVID-19 who have a negative NPS or in difficult-to-diagnose COVID-19 patients.

Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis

Successful detection of the first SARS-CoV-2 cases using the real-time polymerase chain reaction (real-time PCR) method reflects the power and usefulness of this technique. Real-time PCR is a variation of the PCR assay to allow monitoring of the PCR progress in actual time. PCR itself is a molecular process used to enzymatically synthesize copies in multiple amounts of a selected DNA region for various purposes. Real-time PCR is currently one of the most powerful molecular approaches and is widely used in biological sciences and medicine because it is quantitative, accurate, sensitive, and rapid. Current applications of real-time PCR include gene expression analysis, mutation detection, detection and quantification of pathogens, detection of genetically modified organisms, detection of allergens, monitoring of microbial degradation, species identification, and determination of parasite fitness. The technique has been used as a gold standard for COVID-19 diagnosis. Modifications of the standard real-time PCR methods have also been developed for particular applications. This review aims to provide an overview of the current applications of the real-time PCR technique, including its role in detecting emerging viruses such as SARS-CoV-2.

Two Years into the COVID-19 Pandemic: Lessons Learned

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.

A Novel Framework for Modeling Person-to-Person Transmission of Respiratory Diseases

From the beginning of the COVID-19 pandemic, researchers assessed the impact of the disease in terms of loss of life, medical load, economic damage, and other key metrics of resiliency and consequence mitigation; these studies sought to parametrize the critical components of a disease transmission model and the resulting analyses were informative but often lacked critical parameters or a discussion of parameter sensitivities. Using SARS-CoV-2 as a case study, we present a robust modeling framework that considers disease transmissibility from the source through transport and dispersion and infectivity. The framework is designed to work across a range of particle sizes and estimate the generation rate, environmental fate, deposited dose, and infection, allowing for end-to-end analysis that can be transitioned to individual and population health models. In this paper, we perform sensitivity analysis on the model framework to demonstrate how it can be used to advance and prioritize research efforts by highlighting critical parameters for further analyses.

Mechanisms contributing to adverse outcomes of COVID-19 in obesity

A growing amount of epidemiological data from multiple countries indicate an increased prevalence of obesity, more importantly central obesity, among hospitalized subjects with COVID-19. This suggests that obesity is a major factor contributing to adverse outcome of the disease. As it is a metabolic disorder with dysregulated immune and endocrine function, it is logical that dysfunctional metabolism contributes to the mechanisms behind obesity being a risk factor for adverse outcome in COVID-19. Emerging data suggest that in obese subjects, (a) the molecular mechanisms of viral entry and spread mediated through ACE2 receptor, a multifunctional host cell protein which links to cellular homeostasis mechanisms, are affected. This includes perturbation of the physiological renin-angiotensin system pathway causing pro-inflammatory and pro-thrombotic challenges (b) existent metabolic overload and ER stress-induced UPR pathway make obese subjects vulnerable to severe COVID-19, (c) host cell response is altered involving reprogramming of metabolism and epigenetic mechanisms involving microRNAs in line with changes in obesity, and (d) adiposopathy with altered endocrine, adipokine, and cytokine profile contributes to altered immune cell metabolism, systemic inflammation, and vascular endothelial dysfunction, exacerbating COVID-19 pathology. In this review, we have examined the available literature on the underlying mechanisms contributing to obesity being a risk for adverse outcome in COVID-19.

Effects of hypertonic alkaline nasal irrigation on COVID-19

Objective

The causative agent of COVID-19 is a novel member of coronaviridaes, SARS-CoV-2. It has been reported that the spike (S) protein of SARS-CoV-2 is responsible of infectivity. The S protein is demonstrated to be inactivated under environmental condition, such as hypertonicity and alkaline pH. The aim of the study was to investigate the effect of hypertonic alkaline nasal irrigation (HANI) on SARS-CoV-2.

Methods

Sixty patients divided into two groups. The patients in Group 1 used hydroxychloroquine (HCQ), and the patients in Group 2 used HCQ and HANI. Nasopharyngeal samples were collected at the beginning, on 3rd and 7th day of the PCR test positivity. The nasopharyngeal viral load (NVL) changes analyzed with quantitative PCR.

Results

NVL decrease in weekly period was statistically significant for both groups, when the difference between NVL day 0 and 3rd in Group 1 and NVL difference between day 0 and 3rd in Group 2 were compared. The difference between Groups 1 and 2 in terms of NVL change was statistically significant (P < 0.05).

Conclusion

We demonstrated a significant decrease in nasopharyngeal SARS-CoV-2 load with HANI solution and suggest that HANI may be promising modality for the COVID-19 treatment.

Level of evidence

IB.

Virus transmission by ultrasonic scaler and its prevention by antiviral agent: an in vitro study

Background

It is well recognized that dental procedures represent a potential way of infection transmission. With the COVID‐19 pandemic, the focus of dental procedure associated transmission has rapidly changed from bacteria to viruses. The aim was to develop an experimental setup for testing the spread of viruses by ultrasonic scaler (USS) generated dental spray and evaluate its mitigation by antiviral coolants.

Methods

In a virus transmission tunnel, the dental spray was generated by USS with saline coolant and suspension of Equine Arteritis Virus (EAV) delivered to the USS tip. Virus transmission by settled droplets was evaluated with adherent RK13 cell lines culture monolayer. The suspended droplets were collected by a cyclone aero‐sampler. Antiviral activity of 0.25% NaOCl and electrolyzed oxidizing water (EOW) was tested using a suspension test. Antiviral agents' transmission prevention ability was evaluated by using them as a coolant.

Results

In the suspension test with 0.25% NaOCl or EOW, the TCID50/mL was below the detection limit after 5 seconds. With saline coolant, the EAV‐induced cytopathic effect on RK13 cells was found up to the distance of 45 cm, with the number of infected cells decreasing with distance. By aero‐sampler, viral particles were detected in concentration ≤4.2 TCID50/mL. With both antiviral agents used as coolants, no EAV‐associated RK‐13 cell infection was found.

Conclusion

We managed to predictably demonstrate EAV spread by droplets because of USS action. More importantly, we managed to mitigate the spread by a simple substitution of the USS coolant with NaOCl or EOW.

Results from Observational Studies in Real Therapeutic Practice in Patients with Covid-19

The aim of the present work is to summarize the available data from observational studies performed in a real clinical setting of patients with active COVID-19 infection.A systematic review of publications in the scientific medical literature was conducted during the period from the beginning of the infection to the end of June, 2021. All of the 28 publications included in this review are full-text, observational studies published in English, conducted in a real clinical environment and present data on patients, who have been infected with COVID-19. Out of the 28 studies, 4 reviewed the possibility of a mother to infect her newborn during pregnancy or breastfeeding and found no risk to children. One study was related to children and adolescents of all races and included also patients with MIS-C and comorbidities. Non-invasive mechanical ventilation (HFNC) with a nasal cannula in patients with respiratory failure has been also explored and was reported to lead to a positive outcome. Three papers were dedicated to assessment of COVID-19 Standard of Care (SoC), in particular administration of hydroxychloroquine and doxycycline, favipiravir and remdesivir. Another three articles reviewed a large cohort of hospitalized patients with COVID-19. The mortality was higher in patients who were in the ICU. Observational studies of patients with COVID-19 in a real life setting are relatively limited, but provide valuable information on the risks of the disease in adults, children and newborns, as well as the treatment of complications of the infection.

Immune Responses against SARS-CoV-2-Questions and Experiences

Understanding immune reactivity against SARS-CoV-2 is essential for coping with the COVID-19 pandemic. Herein, we discuss experiences and open questions about the complex immune responses to SARS-CoV-2. Some people react excellently without experiencing any clinical symptoms, they do not get sick, and they do not pass the virus on to anyone else ("sterilizing" immunity). Others produce antibodies and do not get COVID-19 but transmit the virus to others ("protective" immunity). Some people get sick but recover. A varying percentage develops respiratory failure, systemic symptoms, clotting disorders, cytokine storms, or multi-organ failure; they subsequently decease. Some develop long COVID, a new pathologic entity similar to fatigue syndrome or autoimmunity. In reality, COVID-19 is considered more of a systemic immune-vascular disease than a pulmonic disease, involving many tissues and the central nervous system. To fully comprehend the complex clinical manifestations, a profound understanding of the immune responses to SARS-CoV-2 is a good way to improve clinical management of COVID-19. Although neutralizing antibodies are an established approach to recognize an immune status, cellular immunity plays at least an equivalent or an even more important role. However, reliable methods to estimate the SARS-CoV-2-specific T cell capacity are not available for clinical routines. This deficit is important because an unknown percentage of people may exist with good memory T cell responsibility but a low number of or completely lacking peripheral antibodies against SARS-CoV-2. Apart from natural immune responses, vaccination against SARS-CoV-2 turned out to be very effective and much safer than naturally acquired immunity. Nevertheless, besides unwanted side effects of the currently available vector and mRNA preparations, concerns remain whether these vaccines will be strong enough to defeat the pandemic. Altogether, herein we discuss important questions, and try to give answers based on the current knowledge and preliminary data from our laboratories.

Estimating salivary carriage of severe acute respiratory syndrome coronavirus 2 in nonsymptomatic people and efficacy of mouthrinse in reducing viral load: A randomized controlled trial

Background

Many people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) never develop substantial symptoms. With more than 34 million people in the United States already infected and highly transmissible variants rapidly emerging, it is highly probable that post- and presymptomatic people will form an important fraction of those seeking dental care. Salivary carriage rates in these populations are not known. Moreover, although preventing transmission is critical for controlling spread, the efficacy of mouthrinses in reducing oral viral load is poorly studied.

Methods

The authors recruited 201 asymptomatic, presymptomatic, postsymptomatic, and symptomatic people and measured copy numbers of SARS-CoV-2 in unstimulated saliva using real-time reverse transcriptase quantitative polymerase chain reaction. Subsequently, the authors inducted 41 symptomatic people into a randomized, triple-blinded study and instructed them to rinse with saline, 1% hydrogen peroxide, 0.12% chlorhexidine, or 0.5% povidone-iodine for 60 seconds. The authors measured viral load 15 and 45 minutes after rinsing.

Results

Salivary SARS-CoV-2 was detected in 23% of asymptomatic, 60% of postsymptomatic, and 28% of presymptomatic participants. Neither carriage rate nor viral load correlated with COVID-19 symptomatology, age, sex, or race or ethnicity. All 4 mouthrinses decreased viral load by 61% through 89% at 15 minutes and by 70% through 97% at 45 minutes. The extent of reduction correlated significantly with initial viral load.

Conclusions

Nonsymptomatic people can pose a risk of transmitting the virus, and mouthrinses are simple and efficacious means of reducing this risk, especially when the load is less than 10⁴ copies per milliliter.

Practical Implications

At a time when resources are stretched, the findings of this study contribute to evidence-based selection of personal protection equipment and simple infection-control practices to reduce contagion at source.

This clinical trial was registered at ClinicalTrials.gov. The registration number is NCT04603794.

Lewis and ABO histo-blood types and the secretor status of patients hospitalized with COVID-19 implicate a role for ABO antibodies in susceptibility to infection with SARS-CoV-2

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) targets the respiratory and gastric epithelium, causing coronavirus disease 2019 (COVID-19). Tissue antigen expression variations influence host susceptibility to many infections. This study aimed to investigate the closely linked Lewis (FUT3) and ABO histo-blood types, including secretor (FUT2) status, to infections with SARS-CoV-2 and the corresponding severity of COVID-19.

STUDY DESIGN AND METHODS

Patients (Caucasians, n = 338) were genotyped for ABO, FUT3, and FUT2, and compared to a reference population of blood donors (n = 250,298). The association between blood types and severity of COVID-19 was addressed by dividing patients into four categories: hospitalized individuals in general wards, patients admitted to the intensive care unit with and without intubation, and deceased patients. Comorbidities were considered in subsequent analyses.

RESULTS

Patients with blood type Lewis (a-b-) or O were significantly less likely to be hospitalized (odds ratio [OR] 0.669, confidence interval [CI] 0.446-0.971, OR 0.710, CI 0.556-0.900, respectively), while type AB was significantly more prevalent in the patient cohort (OR 1.519, CI 1.014-2.203). The proportions of secretors/nonsecretors, and Lewis a+ or Lewis b+ types were consistent between patients and controls. The analyzed blood groups were not associated with the clinical outcome as defined.

DISCUSSION

Blood types Lewis (a-b-) and O were found to be protective factors, whereas the group AB is suggested to be a risk factor for COVID-19. The antigens investigated may not be prognostic for disease severity, but a role for ABO isoagglutinins in SARS-CoV-2 infections is strongly suggested.

Imprints of Lockdown and Treatment Processes on the Wastewater Surveillance of SARS-CoV-2: A Curious Case of Fourteen Plants in Northern India

The present study investigated the detection of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) genomes at each treatment stage of 14 aerobic wastewater treatment plants (WWTPs) serving the major municipalities in two states of Rajasthan and Uttarakhand in Northern India. The untreated, primary, secondary and tertiary treated wastewater samples were collected over a time frame ranging from under-lockdown to post-lockdown conditions. The results showed that SARS-CoV-2 RNA was detected in 13 out of 40 wastewater samples in Jaipur district, Rajasthan and in 5 out of 14 wastewater samples in the Haridwar District, Uttarakhand with the E gene predominantly observed as compared to the N and RdRp target genes in later time-points of sampling. The Ct values of genes present in wastewater samples were correlated with the incidence of patient and community cases of COVID-19. This study further indicates that the viral RNA could be detected after the primary treatment but was not present in secondary or tertiary treated samples. This study implies that aerobic biological wastewater treatment systems such as moving bed biofilm reactor (MBBR) technology and sequencing batch reactor (SBR) are effective in virus removal from the wastewater. This work might present a new indication that there is little to no risk in relation to SARS-CoV-2 while reusing the treated wastewater for non-potable applications. In contrast, untreated wastewater might present a potential route of viral transmission through WWTPs to sanitation workers and the public. However, there is a need to investigate the survival and infection rates of SARS-CoV-2 in wastewater.

Diabetes and Oral Health: Summary of Current Scientific Evidence for Why Transdisciplinary Collaboration Is Needed

This Perspective provides a brief summary of the scientific evidence for the often two-way links between hyperglycemia, including manifest diabetes mellitus (DM), and oral health. It delivers in a nutshell examples of current scientific evidence for the following oral manifestations of hyperglycemia, along with any available evidence for effect in the opposite direction: periodontal diseases, caries/periapical periodontitis, tooth loss, peri-implantitis, dry mouth (xerostomia/hyposalivation), dysbiosis in the oral microbiome, candidiasis, taste disturbances, burning mouth syndrome, cancer, traumatic ulcers, infections of oral wounds, delayed wound healing, melanin pigmentation, fissured tongue, benign migratory glossitis (geographic tongue), temporomandibular disorders, and osteonecrosis of the jaw. Evidence for effects on quality of life will also be reported. This condensed overview delivers the rationale and sets the stage for the urgent need for delivery of oral and general health care in patient-centered transdisciplinary collaboration for early detection and management of both hyperglycemia and oral diseases to improve quality of life.

SARS-CoV-2 (COVID-19), viral load and clinical outcomes; lessons learned one year into the pandemic: A systematic review

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is diagnosed via real time reverse transcriptase polymerase chain reaction (RT-PCR) and reported as a binary assessment of the test being positive or negative. High SARS-CoV-2 viral load is an independent predictor of disease severity and mortality. Quantitative RT-PCR may be useful in predicting the clinical course and prognosis of patients diagnosed with coronavirus disease 2019 (COVID-19).

AIM

To identify whether quantitative SARS-CoV-2 viral load assay correlates with clinical outcome in COVID-19 infections.

METHODS

A systematic literature search was undertaken for a period between December 30, 2019 to December 31, 2020 in PubMed/MEDLINE using combination of terms "COVID-19, SARS-CoV-2, Ct values, Log10 copies, quantitative viral load, viral dynamics, kinetics, association with severity, sepsis, mortality and infectiousness''. After screening 990 manuscripts, a total of 60 manuscripts which met the inclusion criteria were identified. Data on age, number of patients, sample sites, RT-PCR targets, disease severity, intensive care unit admission, mortality and conclusions of the studies was extracted, organized and is analyzed.

RESULTS

At present there is no Food and Drug Administration Emergency Use Authorization for quantitative viral load assay in the current pandemic. The intent of this research is to identify whether quantitative SARS-CoV-2 viral load assay correlates with severity of infection and mortality? High SARS-CoV-2 viral load was found to be an independent predictor of disease severity and mortality in majority of studies, and may be useful in COVID-19 infection in susceptible individuals such as elderly, patients with co-existing medical illness such as diabetes, heart diseases and immunosuppressed. High viral load is also associated with elevated levels of TNF-α, IFN-γ, IL-2, IL-4, IL-6, IL-10 and C reactive protein contributing to a hyper-inflammatory state and severe infection. However there is a wide heterogeneity in fluid samples and different phases of the disease and these data should be interpreted with caution and considered only as trends.

CONCLUSION

Our observations support the hypothesis of reporting quantitative RT-PCR in SARS-CoV-2 infection. It may serve as a guiding principle for therapy and infection control policies for current and future pandemics.

Modeling the early temporal dynamics of viral load in respiratory tract specimens of COVID-19 patients in Incheon, the Republic of Korea

Objective

To investigate the duration and peak of severe acute respiratory syndrome coronavirus 2 shedding as infectivity markers for determining the isolation period.

Methods

A total of 2,558 upper respiratory tract (URT) and lower respiratory tract (LRT) specimens from 138 patients with laboratory-confirmed coronavirus disease were analyzed. Measurements of sequential viral loads were aggregated using the cubic spline smoothing function of a generalized additive model. The time to negative conversion was compared between symptom groups using survival analysis.

Results

In URT samples, viral RNA levels peaked on day 4 after symptom onset and rapidly decreased until day 10 for both E and RdRp genes, whereas those in LRT samples immediately peaked from symptom onset and decreased until days 15.6 and 15.0 for E and RdRp genes, respectively. Median (interquartile range) time to negative conversion was significantly longer in symptomatic (18.0 [13.0–25.0] days) patients than in asymptomatic (13.0 [9.5–17.5] days) patients. The more types of symptoms a patient had, the longer the time to negative conversion.

Conclusions

The viral load rapidly changes depending on the time after symptom onset; the viral shedding period may be longer with more clinical symptoms. Different isolation policies should be applied depending on disease severity.

Diagnostics for SARS-CoV-2 infections

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every corner of the globe, causing societal instability. The resultant coronavirus disease 2019 (COVID-19) leads to fever, sore throat, cough, chest and muscle pain, dyspnoea, confusion, anosmia, ageusia and headache. These can progress to life-threatening respiratory insufficiency, also affecting the heart, kidney, liver and nervous systems. The diagnosis of SARS-CoV-2 infection is often confused with that of influenza and seasonal upper respiratory tract viral infections. Due to available treatment strategies and required containments, rapid diagnosis is mandated. This Review brings clarity to the rapidly growing body of available and in-development diagnostic tests, including nanomaterial-based tools. It serves as a resource guide for scientists, physicians, students and the public at large.

Real-world assessment of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) nasopharyngeal swab testing in a region with a high burden of coronavirus disease 2019 (COVID-19)

Concerns persist regarding possible false-negative results that may compromise COVID-19 containment. Although obtaining a true false-negative rate is infeasible, using real-life observations, the data suggest a possible false-negative rate of ˜2.3%. Use of a sensitive, amplified RNA platform should reassure healthcare systems.

Viral Infectivity in Patients Undergoing Tracheotomy With COVID-19: A Preliminary Study

Objective

To establish the presence of live virus and its association with polymerase chain reaction (PCR) positivity and antibody status in patients with COVID-19 undergoing tracheotomy.

Study Design

Prospective observational study.

Setting

Single institution across 3 hospital sites during the first wave of the COVID-19 pandemic.

Methods

Patients who were intubated for respiratory wean tracheotomy underwent SARS-CoV-2 PCR nasal, throat, and endotracheal tube swabs at the time of the procedure. These were assessed via quantitative real-time reverse transcription PCR. The tracheal tissue excised during the tracheotomy was cultured for SARS-CoV-2 with Vero E6 and Caco2 cells. Serum was assessed for antibody titers against SARS-CoV-2 via neutralization assays.

Results

Thirty-seven patients were included in this study. The mean number of days intubated prior to undergoing surgical tracheotomy was 27.8. At the time of the surgical tracheotomy, PCR swab testing yielded 8 positive results, but none of the 35 individuals who underwent tissue culture were positive for SARS-CoV-2. All 18 patients who had serum sampling demonstrated neutralization antibodies, with a minimum titer of 1:80.

Conclusion

In our series, irrespective of positive PCR swab, the likelihood of infectivity during tracheotomy remains low given negative tracheal tissue cultures. While our results do not undermine national and international guidance on tracheotomy after day 10 of intubation, given the length of time to procedure in our data, infectivity at 10 days cannot be excluded. We do however suggest that a preoperative negative PCR swab not be a prerequisite and that antibody titer levels may serve as a useful adjunct for assessment of infectivity.

Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19

BACKGROUND

Effective management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires large-scale testing to identify and isolate infectious carriers. Self-administered buccal swab and saliva collection are convenient, painless, and safe alternatives to the current healthcare worker (HCW)-collected nasopharyngeal swab (NPS).

METHODS

A cross-sectional single-centre study was conducted on 42 participants who had tested positive for SARS-CoV-2 via an NPS within the past 7 days. Real-time polymerase chain reaction (RT-PCR) was performed and cycle threshold (Ct) values were obtained for each test. The positive percent agreement (PPA), negative percent agreement (NPA), and overall agreement (OA) were calculated for the saliva samples and buccal swabs, and compared with NPS.

RESULTS

Among the 42 participants, 73.8% (31/42) tested positive by any one of the three tests. With reference to NPS, the saliva test had PPA 66.7%, NPA 91.7%, and OA 69.0%; the buccal swab had PPA 56.7%, NPA 100%, and OA 73.8%.

CONCLUSION

Self-collected saliva tests and buccal swabs showed only moderate agreement with HCW-collected NPS. Primary screening for SARS-CoV-2 may be performed with a saliva test or buccal swab, with a negative test warranting a confirmatory NPS to avoid false-negatives, minimize discomfort, and reduce the risk of spread to the community and HCWs.

COVID-19: Test, Test and Test

A new virus was identified in late December 2019 when China reported the first cases of pneumonia in Wuhan, and a global COVID-19 pandemic followed. The world was not late to respond, with a number of sweeping measures ranging from social distancing protocols, stringent hygienic practices, and nation-wide lockdowns, as well as COVID-19 testing campaigns in an attempt to prevent the transmission of the disease and contain the pandemic. Currently, different types of diagnostic testing have been adopted globally, such as nucleic acid detection tests, immunological tests and imaging approaches; however, real-time reverse transcriptase–polymerase chain reaction (RT-PCR) remains the “gold standard” for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pre-analytical factors, such as specimen selection and collection, are crucial for RT-PCR, and any suboptimal collection may contribute to false-negative results. Herein, we address some of the specimen types that have been used in molecular detection methods for COVID-19. However, the pandemic is still evolving, and information might change as more studies are conducted.