Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

Association between the overall burden of comorbidity and Ct values among the older patients with Omicron infection: Mediated by inflammation

Objectives

To investigate the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly with COVID-19.

Methods

We conducted a retrospective observational study. The results of each nucleic acid test of during hospitalization were obtained. Linear regression models assessed the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly. A causal mediation analysis was performed to assess the mediation effects of inflammatory indicators on the association between the overall burden of comorbidity and Ct values.

Results

A total of 767 COVID-19 patients aged ≥ 60 years were included between April 2022 and May 2022. Patients with a high burden of comorbidity had significantly lower Ct values of the ORF gene than subjects with a low burden of comorbidity (median, 24.81 VS 26.58, P < 0.05). Linear regression models showed that a high burden of comorbidity was significantly associated with higher inflammatory responses, including white blood cell count, neutrophil count and C-reactive protein. Also, white blood cell count, neutrophil count, C-reactive protein and the overall burden of comorbidity assessed by age-adjusted Charlson comorbidity index were independent risk factors for the Ct values. A mediation analysis detected the mediation effect of white blood cells on the association between the burden of comorbidity and Ct values, with the indirect effect estimates of 0.381 (95% CI: 0.166, 0.632, P < 0.001). Similarly, the indirect effect of C-reactive protein was -0.307 (95% CI: -0.645, -0.064, P = 0.034). White blood cells and C-reactive protein significantly mediated the relationship between the burden of comorbidity and Ct values by 29.56% and 18.13% of the total effect size, respectively.

Conclusions

Inflammation mediated the association between the overall burden of comorbidity and Ct values among elderly with COVID-19, which suggests that combined immunomodulatory therapies could reduce the Ct values for such patients with a high burden of comorbidity.

Sensitive SARS-CoV-2 salivary antibody assays for clinical saline gargle samples using smartphone-based competitive particle immunoassay platforms

Antibody assay for SARS-CoV-2 has become increasingly important to track latent and asymptomatic infections, check the individual's immune status, and confirm vaccine efficacy and durability. However, current SARS-CoV-2 antibody assays require invasive blood collection, requiring a remote laboratory and a trained phlebotomist. Direct detection of SARS-CoV-2 antibodies from clinical saline gargle samples has been considered challenging due to the smaller number of antibodies in such specimens and the high limit of detection of currently available rapid tests. This work demonstrates simple and non-invasive methods for detecting SARS-CoV-2 salivary antibodies. Competitive particle immunoassays were developed on a paper microfluidic chip using the receptor-binding domain (RBD) antigens on spike proteins. Using a smartphone, they were monitored by counting the captured fluorescent particles or evaluating the capillary flow velocities. The limit of detection (LOD), cross-binding between alpha- and omicron-strains, and the effect of angiotensin-converting enzyme 2 (ACE2) presence were investigated. LODs were 1-5 ng/mL in both 10% and 1% saliva. Clinical saline gargle samples were assayed using both methods, showing a statistical difference between virus-negative and virus-positive samples, although the assays targeted antibodies. Only a small number of virus-positive samples were antibody-negative. The high assay sensitivity detected a small number of antibodies developed even during the early phase of infections. Overall, this work demonstrates the ability to detect SARS-CoV-2 salivary IgG antibodies on simple, cost-effective, portable platforms towards mitigating SARS-CoV-2 and potentially other respiratory viruses.

Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing

The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience is maintained using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. To perform a test, the user loads the sample, closes the device, and reads the result by eye after 60 min. Detecting gamma-irradiated SARS-CoV-2 virions in a mixture of saliva and extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/μL using available antibodies to target the SARS-CoV-2 nucleocapsid protein. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies exhibit limits of detection of 500 copies/μL, 1000 copies/μL, 2000 copies/μL, 2000 copies/μL, and 20,000 copies/μL. By swapping out antibody probes to target different pathogens, amplified HCR lateral flow assays offer a platform for simple, rapid, and sensitive at-home testing for infectious diseases. As an alternative to viral protein detection, we further introduce an HCR lateral flow assay for viral RNA detection.

Intranasal Boosting with Spike Fc-RBD of Wild-Type SARS-CoV-2 Induces Neutralizing Antibodies against Omicron Subvariants and Reduces Viral Load in the Nasal Turbinate of Mice

The emergence of new immune-evasive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and subvariants outpaces the development of vaccines specific against the dominant circulating strains. In terms of the only accepted immune correlate of protection, the inactivated whole-virion vaccine using wild-type SARS-CoV-2 spike induces a much lower serum neutralizing antibody titre against the Omicron subvariants. Since the inactivated vaccine given intramuscularly is one of the most commonly used coronavirus disease 2019 (COVID-19) vaccines in developing regions, we tested the hypothesis that intranasal boosting after intramuscular priming would provide a broader level of protection. Here, we showed that one or two intranasal boosts with the Fc-linked trimeric spike receptor-binding domain from wild-type SARS-CoV-2 can induce significantly higher serum neutralizing antibodies against wild-type SARS-CoV-2 and the Omicron subvariants, including BA.5.2 and XBB.1, with a lower titre in the bronchoalveolar lavage of vaccinated Balb/c mice than vaccination with four intramuscular doses of inactivated whole virion vaccine. The intranasally vaccinated K18-hACE2-transgenic mice also had a significantly lower nasal turbinate viral load, suggesting a better protection of the upper airway, which is the predilected site of infection by Omicron subvariants. This intramuscular priming and intranasal boosting approach that achieves broader cross-protection against Omicron variants and subvariants may lengthen the interval required for changing the vaccine immunogen from months to years.

Lessons learned: A look back at the performance of nine COVID-19 serologic assays and their proposed utility

BACKGROUND

Serologic assays for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been proposed to assist with the acute diagnosis of infection, support epidemiological studies, identify convalescent plasma donors, and evaluate vaccine response.

METHODS

We report an evaluation of nine serologic assays: Abbott (AB) and Epitope (EP) IgG and IgM, EUROIMMUN (EU) IgG and IgA, Roche anti-N (RN TOT) and anti-S (RS TOT) total antibody, and DiaSorin (DS) IgG. We evaluated 291 negative controls (NEG CTRL), 91 PCR positive (PCR POS) patients (179 samples), 126 convalescent plasma donors (CPD), 27 healthy vaccinated donors (VD), and 20 allogeneic hematopoietic stem cell transplant (HSCT) recipients (45 samples).

RESULTS

We observed good agreement with the method performance claims for specificity (93-100%) in NEG CTRL but only 85% for EU IgA. The sensitivity claims in the first 2 weeks of symptom onset was lower (26-61%) than performance claims based on > 2 weeks since PCR positivity. We observed high sensitivities (94-100%) in CPD except for AB IgM (77%), EP IgM (0%). Significantly higher RS TOT was observed for Moderna vaccine recipients then Pfizer (p-values < 0.0001). A sustained RS TOT response was observed for the five months following vaccination. HSCT recipients demonstrated significantly lower RS TOT than healthy VD (p < 0.0001) at dose 2 and 4 weeks after.

CONCLUSIONS

Our data suggests against the use of anti-SARS-CoV-2 assays to aid in acute diagnosis. RN TOT and RS TOT can readily identify past-resolved infection and vaccine response in the absence of native infection. We provide an estimate of expected antibody response in healthy VD over the time course of vaccination for which to compare antibody responses in immunosuppressed patients.

Monitoring of SARS-CoV-2 Infection in Ragusa Area: Next Generation Sequencing and Serological Analysis

The coronavirus disease 19 (COVID-19) post pandemic evolution is correlated to the development of new variants. Viral genomic and immune response monitoring are fundamental to the surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Since 1 January to 31 July 2022, we monitored the SARS-CoV-2 variants trend in Ragusa area sequencing n.600 samples by next generation sequencing (NGS) technology: n.300 were healthcare workers (HCWs) of ASP Ragusa. The evaluation of anti-Nucleocapside (N), receptor-binding domain (RBD), the two subunit of S protein (S1 and S2) IgG levels in 300 exposed vs. 300 unexposed HCWs to SARS-CoV-2 was performed. Differences in immune response and clinical symptoms related to the different variants were investigated. The SARS-CoV-2 variants trend in Ragusa area and in Sicily region were comparable. BA.1 and BA.2 were the most representative variants, whereas the diffusion of BA.3 and BA.4 affected some places of the region. Although no correlation was found between variants and clinical manifestations, anti-N and anti-S2 levels were positively correlated with an increase in the symptoms number. SARS-CoV-2 infection induced a statistically significant enhancement in antibody titers compared to that produced by SARS-CoV-2 vaccine administration. In post-pandemic period, the evaluation of anti-N IgG could be used as an early marker to identify asymptomatic subjects.

Smartphone-based corona virus detection using saliva: A mini-review

During the ongoing worldwide epidemic, SARS-CoV-2 has infected millions of individuals and taken the lives of numerous victims. It is clear that early detection of infected individuals, especially asymptomatic carriers, is possible with the development of innovative analytical tools for rapid identification of COVID-19 present in nasopharyngeal swabs, serum, and saliva. The saliva, as a diagnostic sample, can be easily collected by the patient with almost no discomfort and needs specialized healthcare personnel to manage, which reduces the risks for the operator. Moreover, smartphone-based sensing systems are one of the most attractive techniques that can speed up the detection time of COVID-19 agents without the need for professional staff and clinical centers. In this review, recent advances in precise salivary-based SARS-CoV-2 diagnosis using smartphones via viral RNA detection, antibody identification, and viral antigen identification were summarized. Finally, the conclusion and future perspective of this field are described in brief.

Proactive Contact Tracing

The COVID-19 pandemic has spurred an unprecedented demand for interventions that can reduce disease spread without excessively restricting daily activity, given negative impacts on mental health and economic outcomes. Digital contact tracing (DCT) apps have emerged as a component of the epidemic management toolkit. Existing DCT apps typically recommend quarantine to all digitally-recorded contacts of test-confirmed cases. Over-reliance on testing may, however, impede the effectiveness of such apps, since by the time cases are confirmed through testing, onward transmissions are likely to have occurred. Furthermore, most cases are infectious over a short period; only a subset of their contacts are likely to become infected. These apps do not fully utilize data sources to base their predictions of transmission risk during an encounter, leading to recommendations of quarantine to many uninfected people and associated slowdowns in economic activity. This phenomenon, commonly termed as "pingdemic," may additionally contribute to reduced compliance to public health measures. In this work, we propose a novel DCT framework, Proactive Contact Tracing (PCT), which uses multiple sources of information (e.g. self-reported symptoms, received messages from contacts) to estimate app users' infectiousness histories and provide behavioral recommendations. PCT methods are by design proactive, predicting spread before it occurs. We present an interpretable instance of this framework, the Rule-based PCT algorithm, designed via a multi-disciplinary collaboration among epidemiologists, computer scientists, and behavior experts. Finally, we develop an agent-based model that allows us to compare different DCT methods and evaluate their performance in negotiating the trade-off between epidemic control and restricting population mobility. Performing extensive sensitivity analysis across user behavior, public health policy, and virological parameters, we compare Rule-based PCT to i) binary contact tracing (BCT), which exclusively relies on test results and recommends a fixed-duration quarantine, and ii) household quarantine (HQ). Our results suggest that both BCT and Rule-based PCT improve upon HQ, however, Rule-based PCT is more efficient at controlling spread of disease than BCT across a range of scenarios. In terms of cost-effectiveness, we show that Rule-based PCT pareto-dominates BCT, as demonstrated by a decrease in Disability Adjusted Life Years, as well as Temporary Productivity Loss. Overall, we find that Rule-based PCT outperforms existing approaches across a varying range of parameters. By leveraging anonymized infectiousness estimates received from digitally-recorded contacts, PCT is able to notify potentially infected users earlier than BCT methods and prevent onward transmissions. Our results suggest that PCT-based applications could be a useful tool in managing future epidemics.

Spread of viruses, which measures are the most apt to control COVID-19?

The persistent debate about the modes of transmission of SARS-CoV2 and preventive measures has illustrated the limits of our knowledge regarding the measures to be implemented in the face of viral risk. Past and present (pandemic-related) scientific data underline the complexity of the phenomenon and its variability over time. Several factors contribute to the risk of transmission, starting with incidence in the general population (i.e., colonization pressure) and herd immunity. Other major factors include intensity of symptoms, interactions with the reservoir (proximity and duration of contact), the specific characteristics of the virus(es) involved, and a number of unpredictable elements (humidity, temperature, ventilation…). In this review, we will emphasize the difficulty of "standardizing" the situations that might explain the discrepancies found in the literature. We will show that the airborne route remains the main mode of transmission. Regarding preventive measures of prevention, while vaccination remains the cornerstone of the fight against viral outbreaks, we will remind the reader that wearing a mask is the main barrier measure and that the choice of type of mask depends on the risk situations. Finally, we believe that the recent pandemic should induce us in the future to modify our recommendations by adapting our measures in hospitals, not to the pathogen concerned, which is currently the case, but rather to the type of at-risk situation.

Pilot Study Results on Antibodies to the S- and N-Proteins of SARS-CoV-2 in Paired Sera from COVID-19 Patients with Varying Severity

In this retrospective cohort study, we investigated the formation of individual classes of antibodies to SARS-CoV-2 in archived serial sera from hospitalized patients with the medium–severe (n = 17) and severe COVID-19 (n = 11). The serum/plasma samples were studied for the presence of IgG, IgM and IgA antibodies to the recombinant S- and N-proteins of SARS-CoV-2. By the 7th day of hospitalization, an IgG increase was observed in patients both with a positive PCR test and without PCR confirmation of SARS-CoV-2 infection. Significant increases in the anti-spike IgG levels were noted only in moderate COVID-19. The four-fold increase of IgM to N-protein was obtained more often in the groups with mild and moderate infections. The IgA levels decreased during the infection to both the S- and N-proteins, and the most pronounced decrease was in the severe COVID-19 patients. The serum IgG to S-protein one week after hospitalization demonstrated a high-power relationship (rs = 0.75) with the level of RBD antibodies. There was a medium strength relationship between the levels of CRP and IgG (rs = 0.43). Thus, in patients with acute COVID-19, an increase in antibodies can develop as early as 1 week of hospital stay. The SARS-CoV-2 antibody conversions may confirm SARS-CoV-2 infection in PCR-negative patients.

A Polysaccharide-RBD-Fc-Conjugated COVID-19 Vaccine, SCTV01A, Showed High Immunogenicity and Low Toxicity in Animal Models

We previously developed a polysaccharide--RBD-conjugated nanoparticle vaccine which induced protective efficacy against SARS-CoV-2 in a mouse model. Here, we newly developed a vaccine, SCTV01A, by chemically conjugating recombinant SARS-CoV-2 RBD-Fc and PPS14 (Streptococcus pneumoniae serotype type 14 capsular polysaccharide). The immunogenicity and toxicity of SCTV01A were evaluated in animal models. The PPS14 conjugation enhanced the immunogenicity of RBD-Fc in C57BL/6 mice whether formulated with SCT-VA02B or Alum adjuvant. SCTV01A also induced high opsonophagocytic activity (OPA) against S. pneumoniae serotype 14. In addition, SCTV01A stimulated potent neutralizing titers in rhesus macaques and effectively reduced lung inflammation after SARS-CoV-2 infection with neither antibody-dependent enhancement (ADE) nor vaccine-enhanced diseases (VED) phenomenon. Importantly, the long-term toxicity study of SCTV01A in rhesus macaques did not cause any abnormal toxicity and was tolerated at the highest tested dose (120 μg). The existing immunogenicity and toxicological evaluation results have demonstrated the safety and efficacy of SCTV01A, which will be a promising and feasible vaccine to protect against SARS-CoV-2 infection.

Evaluation of the Rapid Antigen Detection Test for Diagnosing SARS-CoV-2 during the COVID-19 Pandemic: Experience from a Centralized Isolation Site in Shanghai, China

Rapid and reliable diagnosis is important for the management of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid antigen detection test (RADT) is a rapid, inexpensive, and easy method. Several studies have reported that RADTs performed well in many countries; however, very few studies have been reported in China. In this study, we assessed the performance of the RADT (Ediagnosis COVID-19 antigen test kit). This study was conducted in a centralized isolation site in Shanghai and enrolled 716 patients with COVID-19 and 203 noninfected participants. Nasopharyngeal swabs from all participants were collected on the same day and tested using the RADT and real-time reverse transcription-PCR (RT-PCR). The performance of the RADT was evaluated in different scenarios, such as threshold cycle (C_T) values, symptomatic phase, and symptoms on the day of testing. The results demonstrated that the sensitivity for patients with C_T values lower than 20 was 96.55% (95% confidence interval [CI], 87.05 to 99.4). The sensitivities were 78.4% (95% CI, 69.96 to 85.05) for participants within 5 days after the first RT-PCR-positive result and 90.77% (95% CI, 80.34 to 96.19) within 5 days after symptom onset. Moreover, the sensitivity of the RADT was more than 80% for patients with symptoms on the day of testing, including fever (89.29%), cough (86.84%), stuffy nose (92.59%), runny nose (92%), sore throat (81.25%), and muscle pain (80.77%), especially for those with upper respiratory tract symptoms. The specificity of the RADT was good in all scenarios. During the SARS-CoV-2 epidemic, Ediagnosis performed excellently in individuals with a higher viral load (evidenced by lower C_T values), individuals in the early symptomatic phase, and especially those with upper respiratory tract symptoms. IMPORTANCE RADTs have demonstrated excellent performance in many counties for screening SARS-CoV-2 infection, but very few studies have been conducted in China. The performance of RADTs is largely related to different real-life scenarios. In our study, the performance of the RADT was evaluated in different scenarios, such as C_T values, symptomatic phase, and symptoms on the day of testing. The results demonstrated that Ediagnosis (an RADT made in China) performed excellently for individuals with a higher viral load (evidenced by lower C_T values), individuals in the early symptomatic phase, and especially those with upper respiratory tract symptoms.

Real-world utilization of SARS-CoV-2 serological testing in RNA positive patients across the United States

BACKGROUND

As diagnostic tests for COVID-19 were broadly deployed under Emergency Use Authorization, there emerged a need to understand the real-world utilization and performance of serological testing across the United States.

METHODS

Six health systems contributed electronic health records and/or claims data, jointly developed a master protocol, and used it to execute the analysis in parallel. We used descriptive statistics to examine demographic, clinical, and geographic characteristics of serology testing among patients with RNA positive for SARS-CoV-2.

RESULTS

Across datasets, we observed 930,669 individuals with positive RNA for SARS-CoV-2. Of these, 35,806 (4%) were serotested within 90 days; 15% of which occurred <14 days from the RNA positive test. The proportion of people with a history of cardiovascular disease, obesity, chronic lung, or kidney disease; or presenting with shortness of breath or pneumonia appeared higher among those serotested compared to those who were not. Even in a population of people with active infection, race/ethnicity data were largely missing (>30%) in some datasets-limiting our ability to examine differences in serological testing by race. In datasets where race/ethnicity information was available, we observed a greater distribution of White individuals among those serotested; however, the time between RNA and serology tests appeared shorter in Black compared to White individuals. Test manufacturer data was available in half of the datasets contributing to the analysis.

CONCLUSION

Our results inform the underlying context of serotesting during the first year of the COVID-19 pandemic and differences observed between claims and EHR data sources-a critical first step to understanding the real-world accuracy of serological tests. Incomplete reporting of race/ethnicity data and a limited ability to link test manufacturer data, lab results, and clinical data challenge the ability to assess the real-world performance of SARS-CoV-2 tests in different contexts and the overall U.S. response to current and future disease pandemics.

Performance Evaluation of RapiSure (EDGC) COVID-19 S1 RBD IgG/Neutralizing Ab Test for the Rapid Detection of SARS-CoV-2 Antibodies

The accurate detection of anti-neutralizing SARS-CoV-2 antibodies can aid in the understanding of the development of protective immunity against COVID-19. This study evaluated the diagnostic performance of the RapiSure (EDGC) COVID-19 S1 RBD IgG/Neutralizing Ab Test. Using the 90% plaque reduction neutralization test (PRNT₉₀) as a reference, 200 serum samples collected from 78 COVID-19-positive and 122 COVID-19-negative patients were divided into 76 PRNT₉₀-positive and 124 PRNT₉₀-negative groups. The ability of the RapiSure test to detect antibodies was compared to that of the STANDARD Q COVID-19 IgM/IgG Plus test and that of PRNT₉₀. The positive, negative, and overall percent agreement between the RapiSure and STANDARD Q test was 95.7%, 89.3%, and 91.5%, respectively, with a Cohen's kappa of 0.82. The RapiSure neutralizing antibody test results revealed a sensitivity of 93.4% and a specificity of 100% compared to the PRNT results, with an overall percent agreement of 97.5% and Cohen's kappa of 0.95. The diagnostic performance of the RapiSure test was in good agreement with the STANDARD Q COVID-19 IgM/IgG Plus test and comparable to that of the PRNT. The RapiSure S1 RBD IgG/Neutralizing Ab Test was found to be convenient and reliable and, thus, can provide valuable information for rapid clinical decisions during the COVID-19 pandemic.

Humoral SARS-CoV-2 Immune Response in COVID-19 Recovered Vaccinated and Unvaccinated Individuals Related to Post-COVID-Syndrome

BACKGROUND

The duration of anti-SARS-CoV-2-antibody detectability up to 12 months was examined in individuals after either single convalescence or convalescence and vaccination. Moreover, variables that might influence an anti-RBD/S1 antibody decline and the existence of a post-COVID-syndrome (PCS) were addressed.

METHODS

Forty-nine SARS-CoV-2-qRT-PCR-confirmed participants completed a 12-month examination of anti-SARS-CoV-2-antibody levels and PCS-associated long-term sequelae. Overall, 324 samples were collected. Cell-free DNA (cfDNA) was isolated and quantified from EDTA-plasma. As cfDNA is released into the bloodstream from dying cells, it might provide information on organ damage in the late recovery of COIVD-19. Therefore, we evaluated cfDNA concentrations as a biomarker for a PCS. In the context of antibody dynamics, a random forest-based logistic regression with antibody decline as the target was performed and internally validated.

RESULTS

The mean percentage dynamic related to the maximum measured value was 96 (±38)% for anti-RBD/S1 antibodies and 30 (±26)% for anti-N antibodies. Anti-RBD/S1 antibodies decreased in 37%, whereas anti-SARS-CoV-2-anti-N antibodies decreased in 86% of the subjects. Clinical anti-RBD/S1 antibody decline prediction models, including vascular and other diseases, were cross-validated (highest AUC 0.74). Long-term follow-up revealed no significant reduction in PCS prevalence but an increase in cognitive impairment, with no indication for cfDNA as a marker for a PCS.

CONCLUSION

Long-term anti-RBD/S1-antibody positivity was confirmed, and clinical parameters associated with declining titers were presented. A fulminant decrease in anti-SARS-CoV-2-anti-N antibodies was observed (mean change to maximum value 30 (±26)%). Anti-RBD/S1 antibody titers of SARS-CoV-2 recovered subjects boosted with a vaccine exceeded the maximum values measured after single infection by 235 ± 382-fold, with no influence on preexisting PCS. PCS long-term prevalence was 38.6%, with an increase in cognitive impairment compromising the quality of life. Quantified cfDNA measured in the early post-COVID-19 phase might not be an effective marker for PCS identification.

Coronavirus: a comparative analysis of detection technologies in the wake of emerging variants

An outbreak of the coronavirus disease caused by a novel pathogen created havoc and continues to affect the entire world. As the pandemic progressed, the scientific community was faced by the limitations of existing diagnostic methods. In this review, we have compared the existing diagnostic techniques such as reverse transcription polymerase chain reaction (RT-PCR), antigen and antibody detection, computed tomography scan, etc. and techniques in the research phase like microarray, artificial intelligence, and detection using novel materials; on the prospect of sample preparation, detection procedure (qualitative/quantitative), detection time, screening efficiency, cost-effectiveness, and ability to detect different variants. A detailed comparison of different techniques showed that RT-PCR is still the most widely used and accepted coronavirus detection method despite certain limitations (single gene targeting- in context to mutations). New methods with similar efficiency that could overcome the limitations of RT-PCR may increase the speed, simplicity, and affordability of diagnosis. In addition to existing devices, we have also discussed diagnostic devices in the research phase showing high potential for clinical use. Our approach would be of enormous benefit in selecting a diagnostic device under a given scenario, which would ultimately help in controlling the current pandemic caused by the coronavirus, which is still far from over with new variants emerging.

Evaluation of the accuracy in the mucosal detection of anti-SARS-CoV-2 antibodies in nasal secretions and saliva

COVID-19 vaccination with mRNA vaccines induces immune responses capable of neutralizing SARS-CoV-2. Commercially available serological anti-SARS-CoV-2 quantitative and neutralizing assays are essential for the determination of immune responses to vaccines. Nevertheless, at present there is a lack of validated tests to assess the mucosal response to COVID-19 vaccination and standardized analytic and pre-analytic methods have not yet been defined. The aim of our study was to evaluate the accuracy of two diagnostic immunoassays for COVID-19 (ELISA for IgA-S1 and chemiluminescent assay for IgG-RBD) on serum, saliva, and nasal secretions, by the enrollment of three study populations (healthy controls, vaccinated subjects, and subjects recovered from COVID-19 infection). In order to obtain an appropriate cut-off value for the biological matrices studied, ROC curve analyses were performed. Data demonstrate that the analytical and pre-analytical method we have developed can provide accurate and reliable results for the detection of anti-SARS-CoV-2 mucosal specific antibodies (IgA-S1 and IgG-RBD) on saliva and, as a novelty, on nasal secretions, either after COVID-19 infection or in vaccinated subjects.

Differential efficacy and safety of anti-SARS-CoV-2 antibody therapies for the management of COVID-19: a systematic review and network meta-analysis

PURPOSE

To assess and compare the relative efficacy and safety of anti-SARS-CoV-2 antibody regimens for COVID-19.

METHODS

This systematic review and random-effects network meta-analysis was conducted according to PRISMA-NMA. Literature searches were conducted across MEDLINE, EMBASE, PubMed, Web of Science, CENTRAL, and CNKI up to February 20th, 2022. Interventions were ranked using P scores.

RESULTS

Fifty-five RCTs (N = 45,005) were included in the review. Bamlanivimab + etesevimab (OR 0.13, 95% CI 0.02-0.77) was associated with a significant reduction in mortality compared to standard of care/placebo. Casirivimab + imdevimab reduced mortality (OR 0.67, 95% CI 0.50-0.91) in baseline seronegative patients only. Four different regimens led to a significant decrease in the incidence of hospitalization compared to standard of care/placebo with sotrovimab ranking first in terms of efficacy (OR 0.20, 95% CI 0.08-0.48). No treatment improved incidence of mechanical ventilation, duration of hospital/ICU stay, and time to viral clearance. Convalescent plasma and anti-COVID IVIg both led to a significant increase in adverse events compared to standard of care/placebo, but no treatment increased the odds of serious adverse events.

CONCLUSION

Anti-SARS-CoV-2 mAbs are safe, and could be effective in improving mortality and incidence of hospitalization. Convalescent plasma and anti-COVID IVIg were not efficacious and could increase odds of adverse events. Future trials should further examine the effect of baseline seronegativity, disease severity, patient risk factors, and SARS-CoV-2 strain variation on the efficacy of these regimes.

REGISTRATION

PROSPERO-CRD42021289903.

Is safe distance enough to prevent COVID-19? Dispersion and tracking of aerosols in various artificial ventilation conditions using OpenFOAM

The current COVID-19 pandemic has underlined the importance of learning more about aerosols and particles that migrate through the airways when a person sneezes, coughs and speaks. The coronavirus transmission is influenced by particle movement, which contributes to the emergence of regulations on social distance, use of masks and face shield, crowded assemblies, and daily social activity in domestic, public, and corporate areas. Understanding the transmission of aerosols under different micro-environmental conditions, closed, or ventilated, has become extremely important to regulate safe social distances. The present work attempts to simulate the airborne transmission of coronavirus-laden particles under different respiratory-related activities, i.e., coughing and speaking, using CFD modelling through OpenFOAM v8. The dispersion coupled with the Discrete Phase Method (DPM) has been simulated to develop a better understanding of virus carrier particles transmission processes and their path trailing under different ventilation scenarios. The preliminary results of this study with respect to flow fields were in close agreement with published literature, which was then extended under varied ventilation scenarios and respiratory-related activities. The study observed that improper wearing of mask leads to escape of SARS-CoV-2 containminated aerosols having a smaller aerodynamic diameter from the gap between face mask and face, infecting different surfaces in the vicinity. It was also observed that aerosol propagation infecting the area through coughing is a faster phenomenon compared to the propagation of coronavirus-laden particles during speaking. The study's findings will help decision-makers formulate common but differentiated guidelines for safe distancing under different micro-environmental conditions.

Reliability of antibody tests for COVID-19 diagnosis

Objective: The reverse transcription–polymerase chain reaction test (RT-PCR) is the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), and antibody tests are useful as supplemental tools for diagnosis, for measuring the population’s immunity levels, and for checking infection in asymptomatic contacts. This study aimed to evaluate the reliability of five commercial antibody detection test kits. Materials and Methods: The reliability of the Colloidal Gold COVID-19 IgG/IgM Rapid Test Kit, Antibody Rapid Test Hotgen, Beijing Hotgen Biotech Co., Ltd., China), Abbott Chemiluminescent Microparticle Immunoassay (Illinois, USA), Roche Electrochemiluminescence Immunoassay (Roche Diagnostics, Switzerland), Siemens Chemiluminescence (Munich, Germany), and Euroimmun ELISA (Lübeck, Germany) for COVID-19 diagnosis was studied. The antibody-negative group included 50 sera from 2018, and the antibody-positive group included 98 patients with positive RT-PCR results from whom blood samples had been collected 3–9 weeks after hospital discharge. Statistical analysis was performed using SPSS version 23.0 (IBM Corporation, Armonk, NY, USA). The antibody tests’ validity and intra-assay reproducibility were examined, and the Cohen’s kappa coefficients were obtained. The disease prevalence was pegged at 10%. Results: The antibody tests’ sensitivity (69.12–72.46%) and positive predictive values (42.44–100.0%) were low, and their specificity (89.58–100%) and negative predictive values (96.31–97.03%) were high. Their accuracy rates varied from 87.54% to 97.25%, and their intra-assay coefficients of variation varied from 1% to 10%. Conclusion: The agreement between the results of the antibody detection test kits was higher when the kits were classified according to the targeted antigens. The time of blood sample collection, targeted antigens, and antibody types affected the results. Serological tests were found to be useful, and the commercial kits were found to be largely reliable, although, some parameters need to be improved.

Rapid isothermal point-of-care test for screening of SARS-CoV-2 (COVID-19)

Rapid on-site diagnosis of emerging pathogens is key for early identification of infected individuals and for prevention of further spreading in a population. Currently available molecular diagnostic tests are instrument-based whereas rapid antibody and antigen tests are often not sufficiently sensitive for detection in pre-symptomatic subjects. There is a need for rapid point of care molecular screening tests that can be easily adapted to emerging pathogens and are selective, sensitive, reliable in different settings around the world. We have developed a simple, rapid (<30 ​min), and inexpensive test for SARS-CoV-2 that is based on combination of isothermal reverse transcription recombinase polymerase amplification (RT-RPA) using modified primers and visual detection with paper-based microfluidics. Our test (CoRapID) is specific for SARS-CoV-2 (alpha to omicron variants) and does not detect other coronaviruses and pathogens by in silico and in vitro analysis. A two-step test protocol was developed with stable lyophilized reagents that reduces handling by using portable and disposable components (droppers, microapplicators/swabs, paper-strips). After optimization of assay components and conditions, we have achieved a limit of detection (LoD) of 1 copy/reaction by adding a blocking primer to the lateral flow assay. Using a set of 138 clinical samples, a sensitivity of 88.1% (P ​< ​0.05, CI: 78.2-93.8%) and specificity of 93.9% (P ​< ​0.05, CI: 85.4-97.6%) was determined. The lack of need for instrumentation for our CoRapID makes it an ideal on-site primary screening tool for local hospitals, doctors' offices, senior homes, workplaces, and in remote settings around the world that often do not have access to clinical laboratories.

Rapid and Sensitive Diagnosis of COVID-19 Using an Electricity-Free Self-Testing System

Rapid and sensitive detection of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for early diagnosis and effective treatment. Nucleic acid testing has been considered the gold standard method for the diagnosis of COVID-19 for its high sensitivity and specificity. However, the polymerase chain reaction (PCR)-based method in the central lab requires expensive equipment and well-trained personnel, which makes it difficult to be used in resource-limited settings. It highlights the need for a sensitive and simple assay that allows potential patients to detect SARS-CoV-2 by themselves. Here, we developed an electricity-free self-testing system based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) that allows for rapid and accurate detection of SARS-CoV-2. Our system employs a heating bag as the heat source, and a 3D-printed box filled with phase change material (PCM) that successfully regulates the temperature for the RT-LAMP. The colorimetric method could be completed in 40 min and the results could be read out by the naked eye. A ratiometric measurement for exact readout was also incorporated to improve the detection accuracy of the system. This self-testing system is a promising tool for point-of-care testing (POCT) that enables rapid and sensitive diagnosis of SARS-CoV-2 in the real world and will improve the current COVID-19 screening efforts for control and mitigation of the pandemic.

SARS-CoV-2 Detection via RT-PCR in Matched Saliva and Nasopharyngeal Samples Reveals High Concordance in Different Commercial Assays

BACKGROUND

Self-collected saliva samples can increase the diagnostic efficiency and benefit healthcare workers, patient care, and infection control. This study evaluated the performance of self-collected saliva samples compared to nasopharyngeal swabs using three commercial kits for the qualitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS

Matched nasopharyngeal and saliva samples were collected from 103 patients with either asymptomatic or symptomatic COVID-19. Both samples were evaluated using three commercial kits (TaqCheck, Allplex, and TaqPath). To evaluate sample stability, viral RNA extraction was performed in the presence or absence of an RNA-stabilizing solution. Storage conditions, including the duration, temperature, and stability after freezing and thawing of the samples, were also evaluated.

RESULTS

All the saliva samples showed 100% concordance with the nasopharyngeal swab results using TaqCheck and Allplex kits, and 93% using TaqPath kit. No difference was observed in the samples that used the RNA-stabilizing solution compared to the group without the solution. The Ct values of the freeze-thawed samples after 30 days were higher than those on day 0; however, the results were consistent the fresh samples.

CONCLUSION

The high concordance of SARS-CoV-2 detection via reverse transcription-polymerase chain reaction (RT-PCR) in matched saliva and nasopharyngeal samples using different commercial assays reinforces the concept that self-collected saliva samples are non-invasive, rapid, and reliable for diagnosing SARS-CoV-2 infection.

Bioinspired Plasmo-virus for Point-of-Care SARS-CoV-2 Detection

Directly identifying the presence of the virus in infected hosts with an appropriate speed and sensitivity permits early epidemic management even during the presymptomatic incubation period of infection. Here, we synthesize a bioinspired plasmo-virus (BPV) particle for rapid and sensitive point-of-care (POC) detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via a self-assembled plasmonic nanoprobe array on spike proteins. The BPV enables strong near-infrared (NIR) extinction peaks caused by plasmonic nanogaps. We quantify SARS-CoV-2 in viral transport medium (VTM) at low titers within 10 min with a limit of detection (LOD) of 1.4 × 101 pfu/mL, which is 103 times more sensitive than the current gold-standard method. The high-sensitivity and high-speed POC detection may be widely used for the timely, individualized diagnosis of infectious agents in low-resource settings.

Screening and confirmation tests for SARS-CoV-2: benefits and drawbacks

Background

Coronavirus disease 2019 is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that emerged in late 2019 and has activated an ongoing international public health emergency. SARS-CoV-2 was discovered in Wuhan, China, in December 2019 and rapidly spread to other cities and countries. Currently, SARS-CoV-2 diagnostic tests have relied heavily on detecting viral genes, antigens, and human antibodies. Hence, this review discusses and analyses the existing screening and confirmation tests for SARS-CoV-2, including the real-time reverse transcriptase polymerase chain reaction (RT-PCR), lateral flow immunoassay (LFIA), and enzyme-linked immunosorbent assay (ELISA).

Main body

The illustrations of each testing were presented to provide the readers with an understanding of the scientific principles behind the testing methods. The comparison was made by highlighting the advantages and disadvantages of each testing. ELISA is ideal for performing the maximum population screening to determine immunological capacity, although its inability to provide reliable results on the status of the infection. Recently, LFIA has been approved as a quicker way of determining whether a patient is infected at the analysis time without using particular instruments and non-laboratory settings. RT-PCR is the gold-standard approach in terms of sensitivity and specificity.

Conclusion

However, the combination of LFIA or ELISA with RT-PCR is also proposed in this review to obtain an adequate level of sensitivity and specificity.

Graphic Abstract

The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics

Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.

RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid method that can replace RT-qPCR. A simple molecular assay for SARS-CoV-2 RNA detection in gold-standard diagnosis through swabs and alternative specimens such as saliva could be helpful in promoting genomic surveillance. A multicenter study was conducted to evaluate the RT-LAMP assay method as an alternative for the molecular detection of SARS-CoV-2 lineages in swab and saliva samples. A total of 350 swabs from individuals with (n = 276) or without (n = 74) COVID-19 tested by RT-qPCR were collected. Paired saliva was also collected from 90 individuals who had SARS-CoV-2 RNA that was detectable (n = 30) or undetectable (n = 60) via RT-qPCR. For the RT-LAMP methodology, six primers were used for ORF1 gene amplification. As for SARS-CoV-2 genotyping, 39 swabs had the whole genome sequenced by MinION. The sensitivity of RT-LAMP to the swab was 90.2%. For the swab samples with Ct ≤ 30, the sensitivity improved by 96%. Considering saliva with Ct ≤ 30 in RT-qPCR testing, the RT-LAMP sensitivity was 100%. The RT-LAMP specificity was 100% for both the swab and saliva samples. This RT-LAMP assay was capable of detecting all the SARS-CoV-2 lineages circulating in the Brazilian swab samples. The RT-LAMP method has significant potential for use in clinical routines since it was capable of detecting SARS-CoV-2 RNA in swab and saliva samples.

Development and Characterization of Phage Display-Derived Monoclonal Antibodies to the S2 Domain of Spike Proteins of Wild-Type SARS-CoV-2 and Multiple Variants

The rapid emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has resulted in the ongoing global coronavirus disease 2019 (COVID-19) pandemic. Thus, the rapid development of a platform to detect a broad range of SARS-CoV-2 variants is essential for successful COVID-19 management. In this study, four SARS-CoV-2 spike protein-specific single-chain variable fragments (scFvs) were isolated from a synthetic antibody library using phage display technology. Following the conversion of these scFvs into monoclonal antibodies (mAbs) (K104.1-K104.4) and production and purification of the mAbs, the antibody pair (K104.1 and K104.2) that exhibited the highest binding affinity (K104.1 and K104.2, 1.3 nM and 1.9 nM) was selected. Biochemical analyses revealed that this antibody pair specifically bound to different sites on the S2 subunit of the spike protein. Furthermore, we developed a highly sensitive sandwich immunoassay using this antibody pair that accurately and quantitatively detected the spike proteins of wild-type SARS-CoV-2 and multiple variants, including Alpha, Beta, Gamma, Delta, Kappa, and Omicron, in the picomolar range. Conclusively, the novel phage display-derived mAbs we have developed may be useful for the rapid and efficient detection of the fast-evolving SARS-CoV-2.

COVID-19: A Comprehensive Review on Cardiovascular Alterations, Immunity, and Therapeutics in Older Adults

Here, we present a review focusing on three relevant issues related to COVID-19 and its impact in older adults (60 years and older). SARS-CoV-2 infection starts in the respiratory system, but the development of systemic diseases accompanied by severe clinical manifestations has also been reported, with cardiovascular and immune system dysfunction being the major ones. Additionally, the presence of comorbidities and aging represent major risk factors for the severity and poor prognosis of the disease. Since aging-associated decline has been largely related to immune and cardiovascular alterations, we sought to investigate the consequences and the underlying mechanisms of these pathologies to understand the severity of the illness in this population. Understanding the effects of COVID-19 on both systems should translate into comprehensive and improved medical care for elderly COVID-19 patients, preventing cardiovascular as well as immunological alterations in this population. Approved therapies that contribute to the improvement of symptoms and a reduction in mortality, as well as new therapies in development, constitute an approach to managing these disorders. Among them, we describe antivirals, cytokine antagonists, cytokine signaling pathway inhibitors, and vaccines.

Immobilized cellulose nanospheres enable rapid antigen detection in lateral flow immunoassays

Rapid diagnostic systems are essential in controlling the spread of viral pathogens and efficient patient management. The available technologies for low-cost viral antigen testing have several limitations, including a lack of accuracy and sensitivity. Here, we introduce a platform based on cellulose II nanoparticles (oppositely charged NPan and NPcat) for effective control of surface protein interactions, leading to rapid and sensitive antigen tests. Passivation against non-specific adsorption and augmented immobilization of sensing antibodies is achieved by adjusting the electrostatic charge of the nanoparticles. The interactions affecting the performance of the system are investigated by microgravimetry and confocal imaging. As a proof-of-concept test, SARS-CoV-2 nucleocapsid sensing was carried out by using saliva-wicking by channels that were stencil-printed on paper. We conclude that inkjet-printed NPcat elicits strong optical signals, visible after a few minutes, opening the opportunity for cost-effective and rapid diagnostic.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10570-022-05038-y.

Spatial and temporal dynamics of SARS-CoV-2: Modeling, analysis and simulation

A reaction-diffusion viral infection model is formulated to characterize the infection process of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a heterogeneous environment. In the model, the viral production, infection and death rates of compartments are given by the general functions. We consider the well-posedness of the solution, derive the basic reproduction number R 0 , discuss the global stability of uninfected steady state and explore the uniform persistence for the model. We further propose a spatial diffusion SARS-CoV-2 infection model with humoral immunity and spatial independent coefficients, and analyze the global attractivity of uninfected, humoral inactivated and humoral activated equilibria which are determined by two dynamical thresholds. Numerical simulations are performed to illustrate our theoretical results which reveal that diffusion, spatial heterogeneity and incidence types have evident impact on the SARS-CoV-2 infection process which should not be neglected for experiments and clinical treatments.

Comparative evaluation of saliva and nasopharyngeal swab for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia

BACKGROUND

Nasopharyngeal swab (NPS) remains the recommended sample type for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) diagnosis. However, the collection procedure causes discomfort and irritation to the patients, lowering the quality of the sample and exposing healthcare workers to risk. Furthermore, there is also a shortage of flocked swabs and personnel protective equipment in low-income settings. Therefore, this necessitates an alternative diagnostic specimen. The purpose of this study was to evaluate the performance of saliva against NPS for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia.

METHODS

Comparative cross-sectional study was conducted from June 28 to July 30, 2022. A total of 227 paired saliva and NPS samples were collected from 227 COVID-19 suspected patients. Saliva and NPS samples were collected and transported to the Somali Regional Molecular Laboratory. Extraction was conducted using DaAn kit (DaAn Gene Co., Ltd China). Veri-Q RT-qPCR was used for amplification and detection (Mico BioMed Co, Ltd, Republic of Korea). The data were entered into Epi-data version 4.6 and analyzed using SPSS 25. McNemar's test was used to compare the detection rate. Agreement between NPS and saliva was performed using Cohen's Kappa. The mean and median of cycle threshold values were compared using paired t-tests and the correlation between cycle threshold values was measured using Pearson correlation coefficient. P value < 0.05 was considered statistically significant.

RESULTS

The overall positivity rate of SARS-CoV-2 RNA was 22.5% (95% CI 17-28%). Saliva showed higher sensitivity (83.8%, 95% CI, 73-94.5%) than NPS (68.9%, 95% CI 60.8-76.8%). The specificity of saliva was 92.6% (95% CI, 80.6% - 100%) compared to NPS (96.7%, 95% CI, 87% - 100%). The positive, negative, and overall percent agreement between NPS and saliva was 83.8%, 92.6%, and 91.2% respectively (κ = 0.703, 95% CI 0.58-0.825, P = 0.00). The concordance rate between the two samples was 60.8%. NPS showed a higher viral load than saliva. There was low positive correlation between the cycle threshold values of the two samples (r = 0.41, 95% CI -1.69 to -0.98, P >0.05).

CONCLUSION

Saliva showed a higher detection rate for SARS-CoV-2 molecular diagnosis than NPS and there was significant agreement between the two specimens. Therefore, saliva could be suitable and easily obtainable alternative diagnostic specimen for SARS-CoV-2 molecular diagnosis.

COVID-19 (novel SARS-CoV-2) neurological illness

COVID-19 illness is associated with diverse neurological manifestations. Its exceptionally high prevalence results from unprecedented genetic diversity, genomic recombination, and superspreading. With each new mutation and variant, there are foreseeable risks of rising fatality and novel neurological motor complications in childhood and adult cases. This chapter provides an extensive review of COVID-19 neurological illness, notably the motor manifestations. Innovative treatments have been developed to stem the spread of infectious contagious illness, and attenuate the resultant cytokine storm and other postinfectious immune aspects responsible for postacute COVID-19 syndrome due to the multiplier effect of infection, immunity, and inflammation, termed I3.

PCR combined with serologic testing improves the yield and efficiency of SARS-CoV-2 infection hunting: A study in 40,689 consecutive overseas arrivals

Background

The global epidemiological situation of COVID-19 remains serious. The rapid hunting of SARS-CoV-2 infection is the key means for preventing transmission.

Methods

A total of 40,689 consecutive overseas arrivals were screened for SARS-CoV-2 infection based on PCR and serologic testing. The yield and efficiency of different screening algorithms were evaluated.

Result

Among the 40,689 consecutive overseas arrivals, 56 (0.14%) subjects were confirmed to have SARS-CoV-2 infection. The asymptomatic rate was 76.8%. When the algorithm based on PCR alone was used, the identification yield of a single round of PCR (PCR1) was only 39.3% (95% CI: 26.1-52.5%). It took at least four rounds of PCR to achieve a yield of 92.9% (95% CI: 85.9-99.8%). Fortunately, an algorithm based on a single round of PCR combined with a single round of serologic testing (PCR1+ Ab1) greatly improved the screening yield to 98.2% (95% CI: 94.6-100.0%) and required 42,299 PCR and 40,689 serologic tests that cost 6,052,855 yuan. By achieving a similar yield, the cost of PCR1+ Ab1 was 39.2% of that of four rounds of PCR. For hunting one case in PCR1+ Ab1, 769 PCR and 740 serologic tests were required, costing 110,052 yuan, which was 63.0% of that of the PCR1 algorithm.

Conclusion

Comparing an algorithm based on PCR alone, PCR combined with a serologic testing algorithm greatly improved the yield and efficiency of the identification of SARS-CoV-2 infection.

Progress in salivary glands: Endocrine glands with immune functions

The production and secretion of saliva is an essential function of the salivary glands. Saliva is a complicated liquid with different functions, including moistening, digestion, mineralization, lubrication, and mucosal protection. This review focuses on the mechanism and neural regulation of salivary secretion, and saliva is secreted in response to various stimuli, including odor, taste, vision, and mastication. The chemical and physical properties of saliva change dynamically during physiological and pathophysiological processes. Moreover, the central nervous system modulates salivary secretion and function via various neurotransmitters and neuroreceptors. Smell, vision, and taste have been investigated for the connection between salivation and brain function. The immune and endocrine functions of the salivary glands have been explored recently. Salivary glands play an essential role in innate and adaptive immunity and protection. Various immune cells such as B cells, T cells, macrophages, and dendritic cells, as well as immunoglobins like IgA and IgG have been found in salivary glands. Evidence supports the synthesis of corticosterone, testosterone, and melatonin in salivary glands. Saliva contains many potential biomarkers derived from epithelial cells, gingival crevicular fluid, and serum. High level of matrix metalloproteinases and cytokines are potential markers for oral carcinoma, infectious disease in the oral cavity, and systemic disease. Further research is required to monitor and predict potential salivary biomarkers for health and disease in clinical practice and precision medicine.

Mouth rinses efficacy on salivary SARS-CoV-2 viral load: A randomized clinical trial

Considering the global trend to confine the COVID-19 pandemic by applying various preventive health measures, preprocedural mouth rinsing has been proposed to mitigate the transmission risk of SARS-CoV-2 in dental clinics. The study aimed to investigate the effect of different mouth rinses on salivary viral load in COVID-19 patients. This study was a single-center, randomized, double-blind, six-parallel-group, placebo-controlled clinical trial that investigated the effect of four mouth rinses (1% povidone-iodine, 1.5% hydrogen peroxide, 0.075% cetylpyridinium chloride, and 80 ppm hypochlorous acid) on salivary SARS-CoV-2 viral load relative to the distilled water and no-rinse control groups. The viral load was measured by quantitative reverse transcription PCR (RT-qPCR) at baseline and 5, 30, and 60 min post rinsing. The viral load pattern within each mouth rinse group showed a reduction overtime; however, this reduction was only statistically significant in the hydrogen peroxide group. Further, a significant reduction in the viral load was observed between povidone-iodine, hydrogen peroxide, and cetylpyridinium chloride compared to the no-rinse group at 60 min, indicating their late antiviral potential. Interestingly, a similar statistically significant reduction was also observed in the distilled water control group compared to the no-rinse group at 60 min, proposing mechanical washing of the viral particles through the rinsing procedure. Therefore, results suggest using preprocedural mouth rinses, particularly hydrogen peroxide, as a risk-mitigation step before dental procedures, along with strict adherence to other infection control measures.

Unconventional secretion of unglycosylated ORF8 is critical for the cytokine storm during SARS-CoV-2 infection

Coronavirus disease 2019 is a respiratory infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Evidence on the pathogenesis of SARS-CoV-2 is accumulating rapidly. In addition to structural proteins such as Spike and Envelope, the functional roles of non-structural and accessory proteins in regulating viral life cycle and host immune responses remain to be understood. Here, we show that open reading frame 8 (ORF8) acts as messenger for inter-cellular communication between alveolar epithelial cells and macrophages during SARS-CoV-2 infection. Mechanistically, ORF8 is a secretory protein that can be secreted by infected epithelial cells via both conventional and unconventional secretory pathways. Conventionally secreted ORF8 is glycosylated and loses the ability to recognize interleukin 17 receptor A of macrophages, possibly due to the steric hindrance imposed by N-glycosylation at Asn78. However, unconventionally secreted ORF8 does not undergo glycosylation without experiencing the ER-Golgi trafficking, thereby activating the downstream NF-κB signaling pathway and facilitating a burst of cytokine release. Furthermore, we show that ORF8 deletion in SARS-CoV-2 attenuates inflammation and yields less lung lesions in hamsters. Our data collectively highlights a role of ORF8 protein in the development of cytokine storms during SARS-CoV-2 infection.

Antimicrobial efficacy, mode of action and in vivo use of hypochlorous acid (HOCl) for prevention or therapeutic support of infections

The objective is to provide a comprehensive overview of the rapidly developing field of the current state of research on in vivo use of hypochlorous acid (HOCl) to aid infection prevention and control, including naso-pharyngeal, alveolar, topical, and systemic HOCl applications. Also, examples are provided of dedicated applications in COVID-19. A brief background of HOCl's biological and chemical specifics and its physiological role in the innate immune system is provided to understand the effect of in vivo applications in the context of the body's own physiological defense mechanisms.

[Seroprevalence of anti-SARS-CoV-2 IgG antibodies in resident physicians]

Background

COVID-19 pandemic spread around the world swiftly; there are several diagnostic strategies available. Health workers, especially medical residents (MR), are a high-risk population for acquiring this infection.

Objective

To estimate the seroprevalence of antibodies against SARS-CoV-2 and the associated factors in MR of a third level hospital.

Material and methods

330 MR from different specialties were evaluated with a questionnaire and collection of blood samples for analysis by microparticle chemiluminescent immunoassay. The prevalence of previous infection was defined by seropositivity of these antibodies. Descriptive statistics and concordance between the RT-PCR tests and the presence of anti-SARS-CoV-2 IgG were used.

Results

Of 330 MR, 84.5% actively participated in COVID patient care. One out of 3 reported symptoms of COVID-19; in 67.6% the possible site of infection was a hospital setting not associated with the COVID area. Out of 71 symptomatic subjects, 61.9% underwent RT-PCR against SARS-CoV-2; 20 were positive. In 15.8% of the total, the presence of anti-SARS-CoV-2 IgG antibodies was determined. Only 1 out of 3 subjects with a positive PCR had antibodies, and 11.3% of the cases, even with a positive RT-PCR test, did not develop humoral immunity.

Conclusions

The seroprevalence was lower than that reported at the national level, potentially due to protection measures. The main risk factor was contact with the virus in areas of the hospital not related to COVID, making it imperative to reinforce security protocols in those spaces.

Efficacy of mouthrinses in reducing oral SARS-COV-2 load: a review

Accumulated evidence has shown that the oral cavity may be an important reservoir for SARS-CoV-2. Some authors have suggested that the use of mouthrinses could reduce SARS-CoV-2 viral load in the saliva. Thus, the aim of this review was to synthesize evidence about the efficacy of mouthrinses in reducing the salivary viral load of SARS-CoV-2. 2. Nine randomized controlled trials (RCTs) have investigated the efficacy of different mouthrinses in reducing salivary SARS-CoV-2 loads. Various active ingredients have been tested in these trials: 0.5%,1% and 2% povidone-iodine, 0.2% and 0.12% chlorhexidine (CHX), 0.075% cetylpyridinium chloride (CPC), 0.075% CPC with Zinc lactate, 1% and 1.5% hydrogen peroxide (HP), 1.5% HP + 0.12% CHX and ß-cyclodextrin and citrox. The studies reported an intra-group reduction in the salivary levels of the virus, when compared with the baseline. However, the majority of these trials failed to demonstrate a significant inter-group difference between active groups and the control group relative to the decrease in salivary SARS-CoV-2 loads. Although promising, these results should be confirmed by larger trials.

Predicting the response to methylprednisolone pulses in patients with SARS-COV-2 infection

INTRODUCTION

Treating systemic inflammation caused by SARS-COV 2 (COVID-19) has become a challenge for the clinician. Corticosteroids have been the turning point in the treatment of this disease. Preliminary data from Recovery clinical trial raises hope by showing that treatment with dexamethasone at doses of 6 mg/day shows a reduction on morbidity in patients requiring added oxygen therapy. However, both the start day or what kind of corticosteroid, are still questions to be clarified. Since the pandemic beginning, we have observed large differences in the type of corticosteroid, dose and initiation of treatment.Our objective is to assess the predictive capacity of the characteristics of patients treated with methylprednisolone pulses to predict hospital discharge.

MATERIALS AND METHODS

We presented a one-center observational study of a retrospective cohort. We included all patients admitted between 03/06/2020 and 05/15/2020 because of COVID-19. We have a total number of 1469 patients, of whom 322 received pulses of methylprednisolone. Previous analytical, radiographic, previous disease data were analyzed on these patients. The univariant analysis was performed using Chi-squared and the T test of Student according to the qualitative or quantitative nature of the variables respectively. For multivariate analysis, we have used binary logistic regression and ROC curves.

RESULTS

The analysis resulted statistically significant in dyspnea, high blood pressure, dyslipidemia, stroke, ischemic heart disease, cognitive impairment, solid tumor, C-reactive protein (CRP), lymphopenia and d-dimer within 5 days of admission. Radiological progression and FIO₂ input are factors that are associated with a worst prognosis in COVID-19 that receive pulses of methylprednisolone. Multivariate analysis shows that age, dyspnea and C-reactive protein are markers of hospital discharge with an area below the curve of 0.816.

CONCLUSIONS

In patients with methylprednisolone pulses, the capacity of the predictive model for hospital discharge including variables collected at 5 days was (area under the curve) 0.816.

Predicting the response to methylprednisolone pulses in patients with SARS-COV-2 infection

INTRODUCTION

Treating systemic inflammation caused by SARS-COV 2 (COVID-19) has become a challenge for the clinician. Corticosteroids have been the turning point in the treatment of this disease. Preliminary data from Recovery clinical trial raises hope by showing that treatment with dexamethasone at doses of 6mg/day shows a reduction on morbidity in patients requiring added oxygen therapy. However, both the start day or what kind of corticosteroid, are still questions to be clarified. Since the pandemic beginning, we have observed large differences in the type of corticosteroid, dose and initiation of treatment. Our objective is to assess the predictive capacity of the characteristics of patients treated with methylprednisolone pulses to predict hospital discharge.

MATERIALS AND METHODS

We presented a one-center observational study of a retrospective cohort. We included all patients admitted between 03/06/2020 and 05/15/2020 because of COVID-19. We have a total number of 1469 patients, of whom 322 received pulses of methylprednisolone. Previous analytical, radiographic, previous disease data were analyzed on these patients. The univariant analysis was performed using Chi-squared and the T test of Student according to the qualitative or quantitative nature of the variables respectively. For multivariate analysis, we have used binary logistic regression and ROC curves.

RESULTS

The analysis resulted statistically significant in dyspnea, high blood pressure, dyslipidemia, stroke, ischemic heart disease, cognitive impairment, solid tumor, C-reactive protein (CRP), lymphopenia and d-dimer within 5 days of admission. Radiological progression and FIO₂ input are factors that are associated with a worst prognosis in COVID-19 that receive pulses of methylprednisolone. Multivariate analysis shows that age, dyspnea and C-reactive protein are markers of hospital discharge with an area below the curve of 0.816.

CONCLUSIONS

In patients with methylprednisolone pulses, the capacity of the predictive model for hospital discharge including variables collected at 5 days was (area under the curve) 0.816.

Life-threatening pneumothorax after release from isolation with COVID-19 pneumonia

Pneumothorax was previously considered as a complication of severe coronavirus disease 2019 (COVID-19) pneumonia. However, it is now known that pneumothorax can develop in other cases. Here, we describe the case of a patient who developed tension pneumothorax after release from isolation from COVID-19 pneumonia. The patient was admitted to our hospital with severe COVID-19 pneumonia on the 10th day after onset. Ventilatory management was carried out on the first day of admission; however, the patient was weaned off the next day. The treatment course was uneventful. On the morning of discharge from the hospital, the patient experienced sudden dyspnea. Chest radiography revealed a large left-tension pneumothorax with a mediastinal shift to the right. As this finding required immediate attention, a chest tube was inserted. Chest computed tomography (CT) showed an airspace in the left thoracic cavity and subpleural thin-walled cystic lesions, such as bullae in the left lobe. One month later, chest CT showed resolution of the cystic lesions. The development of pneumothorax in COVID-19 pneumonia should be considered not only in cases of severe illness, but also after release from isolation. Recently, revisions to measures against COVID-19 have been considered worldwide, including shortening of the isolation period and reviewing the identification of all cases. This is an educational report demonstrating that life-threatening pneumothorax may develop after release from isolation due to COVID-19 pneumonia.

Coupling the Within-Host Process and Between-Host Transmission of COVID-19 Suggests Vaccination and School Closures are Critical

Most models of COVID-19 are implemented at a single micro or macro scale, ignoring the interplay between immune response, viral dynamics, individual infectiousness and epidemiological contact networks. Here we develop a data-driven model linking the within-host viral dynamics to the between-host transmission dynamics on a multilayer contact network to investigate the potential factors driving transmission dynamics and to inform how school closures and antiviral treatment can influence the epidemic. Using multi-source data, we initially determine the viral dynamics and estimate the relationship between viral load and infectiousness. Then, we embed the viral dynamics model into a four-layer contact network and formulate an agent-based model to simulate between-host transmission. The results illustrate that the heterogeneity of immune response between children and adults and between vaccinated and unvaccinated infections can produce different transmission patterns. We find that school closures play a significant effect on mitigating the pandemic as more adults get vaccinated and the virus mutates. If enough infected individuals are diagnosed by testing before symptom onset and then treated quickly, the transmission can be effectively curbed. Our multiscale model reveals the critical role played by younger individuals and antiviral treatment with testing in controlling the epidemic.

Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes

Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCt_NR) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCt_NR correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCt_NR, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics.

The long-term dynamics of serum antibodies against SARS-CoV-2

Objective

To analyze the long-term dynamics of antibodies against SARS-CoV-2 and understand the impact of age, gender, and viral load on patients' immunological response.

Methods

Serum samples were obtained from 231 COVID-19 positive patients from Macaé, in Rio de Janeiro state, in Brazil, from June 2020 until January 2021. The production of IgA, IgM, IgG, and IgE against S glycoprotein was analyzed using the S-UFRJ assay, taking into account the age, gender, and viral load.

Results

Analysis of antibody production over 7 months revealed that IgA positivity gradually decreased after the first month. Additionally, the highest percentage of IgM positivity occurred in the first month (97% of patients), and declined after this period, while IgG positivity remained homogeneous for all 7 months. The same analysis for IgE revealed that almost all samples were negative. The comparison of antibody production between genders showed no significant difference. Regarding the age factor and antibody production, patients aged ≥60 years produced almost twice more IgA than younger ones (17-39 years old). Finally, a relationship between viral load and antibody production was observed only for older patients.

Conclusions

Our work provides an overview of long-term production of antibodies against SARS-CoV-2, suggesting prolonged production of IgA and IgM antibodies for 3 months and continued IgG production for over 7 months. In addition, it identified a correlation between viral load and IgM titers in the older group and, finally, different IgA production between the age groups.

Tale of the Titers: Serologic Testing for SARS-CoV-2-Yes, No, and Maybe, With Clinical Examples From the IDSA Diagnostics Committee

Diagnosis of acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies on detection of viral antigens or amplified viral nucleic acids. Serology, although invaluable for epidemiology, is not routinely needed clinically. However, in some settings, serologic data may have direct clinical utility: for example, in evaluation of persistent symptoms in patients without a prior diagnosis of acute infection. In contrast, SARS-CoV-2 serologic testing is sometimes used or requested in situations in which existing data do not support it, such as determination of need for vaccination. In this study, we describe available methods of serologic testing and provide cases supported by clinical vignettes of where such tests can be helpful, as well as examples where they are not. These examples may help clarify clinical decision making in this rapidly evolving area.