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

A longitudinal study of anti-SARS-CoV-2 antibody seroprevalence in a random sample of the general population in Hiroshima in 2020

BACKGROUND

This longitudinal study aimed to determine chronological changes in the seroprevalence of prior SARS-CoV-2 infection, including asymptomatic infections in Hiroshima Prefecture, Japan.

METHODS

A stratified random sample of 7,500 residents from five cities of Hiroshima Prefecture was selected to participate in a three-round survey from late 2020 to early 2021, before the introduction of the COVID-19 vaccine. The seroprevalence of anti-SARS-CoV-2 antibodies was calculated if at least two of four commercially available immunoassays were positive. Then, the ratio between seroprevalence and the prevalence of confirmed COVID-19 cases in Hiroshima was calculated and compared to the results from other prefectures where the Ministry of Health, Labour and Welfare conducted a survey by using the same reagents at almost the same period.

RESULTS

The numbers of participants in the first, second, and third rounds of the survey were 3025, 2396, and 2351, respectively and their anti-SARS-CoV-2 antibodies seroprevalences were 0.03% (95% confidence interval: 0.00-0.10%), 0.08% (0.00-0.20%), and 0.30% (0.08-0.52%), respectively. The ratio between the seroprevalence and the prevalence of confirmed COVID-19 cases in Hiroshima was 1.2, which was smaller than that in similar studies in other prefectures.

CONCLUSIONS

The seroprevalence of anti-SARS-CoV-2 antibodies in Hiroshima increased tenfold in a half year. The difference between seroprevalence and the prevalence of confirmed COVID-19 cases in Hiroshima was smaller than that in other prefectures, suggesting that asymptomatic patients were more actively detected in Hiroshima.

Effect of Oral Antiseptics in Reducing SARS-CoV-2 Infectivity: Evidence from a Randomized Double-blind Clinical Trial

Background: In vitro studies have shown that several oral antiseptics have virucidal activity against SARS-CoV-2. Thus, mouthwashes have been proposed as an easy to implement strategy to reduce viral transmission. However, there are no data measuring SARS-CoV-2 viability after mouthwashes in vivo. Methods: In this randomized double-blind, five-parallel-group, placebo-controlled clinical trial, SARS-CoV-2 salivary viral load (by quantitative PCR) and its infectious capacity (incubating saliva in cell cultures) have been evaluated before and after four different antiseptic mouthwashes and placebo in 54 COVID-19 patients. Results: Contrary to in vitro evidence, salivary viral load was not affected by any of the four tested mouthwashes. Viral culture indicated that cetylpyridinium chloride (CPC) significantly reduced viral infectivity, but only at 1-hour post-mouthwash. Conclusion: These results indicate that some of the mouthwashes currently used to reduce viral infectivity are not efficient in vivo and, furthermore, that this effect is not immediate, generating a false sense of security.

Trial registration:ClinicalTrials.gov identifier: NCT04707742..

Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from saliva

Polymerase chain reaction (PCR) has proven to be the gold-standard for SARS-CoV-2 detection in clinical settings. The most common approaches rely on nasopharyngeal specimens obtained from swabs, followed by RNA extraction, reverse transcription and quantitative PCR. Although swab-based PCR is sensitive, swabbing is invasive and unpleasant to administer, reducing patient compliance for regular testing and resulting in an increased risk of improper sampling. To overcome these obstacles, we developed a non-invasive one-step RT-qPCR assay performed directly on saliva specimens. The University of Nottingham Asymptomatic Testing Service protocol simplifies sample collection and bypasses the need for RNA extraction, or additives, thus helping to encourage more regular testing and reducing processing time and costs. We have evaluated the assay against the performance criteria specified by the UK regulatory bodies and attained accreditation (BS EN ISO/IEC 17,025:2017) for SARS-CoV-2 diagnostic testing by the United Kingdom Accreditation Service. We observed a sensitivity of 1 viral copy per microlitre of saliva, and demonstrated a concordance of > 99.4% between our results and those of other accredited testing facilities. We concluded that saliva is a stable medium that allows for a highly precise, repeatable, and robust testing method.

SARS-CoV-2 Spike- and Nucleoprotein-Specific Antibodies Induced After Vaccination or Infection Promote Classical Complement Activation

Antibodies specific for the spike glycoprotein (S) and nucleocapsid (N) SARS-CoV-2 proteins are typically present during severe COVID-19, and induced to S after vaccination. The binding of viral antigens by antibody can initiate the classical complement pathway. Since complement could play pathological or protective roles at distinct times during SARS-CoV-2 infection we determined levels of antibody-dependent complement activation along the complement cascade. Here, we used an ELISA assay to assess complement protein binding (C1q) and the deposition of C4b, C3b, and C5b to S and N antigens in the presence of antibodies to SARS-CoV-2 from different test groups: non-infected, single and double vaccinees, non-hospitalised convalescent (NHC) COVID-19 patients and convalescent hospitalised (ITU-CONV) COVID-19 patients. C1q binding correlates strongly with antibody responses, especially IgG1 levels. However, detection of downstream complement components, C4b, C3b and C5b shows some variability associated with the subject group from whom the sera were obtained. In the ITU-CONV, detection of C3b-C5b to S was observed consistently, but this was not the case in the NHC group. This is in contrast to responses to N, where median levels of complement deposition did not differ between the NHC and ITU-CONV groups. Moreover, for S but not N, downstream complement components were only detected in sera with higher IgG1 levels. Therefore, the classical pathway is activated by antibodies to multiple SARS-CoV-2 antigens, but the downstream effects of this activation may differ depending the disease status of the subject and on the specific antigen targeted.

Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site

Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation sequencing in patients admitted to intensive care unit. A deep sequencing of the S gene of SARS-CoV-2 from 109 clinical specimens, sampled from the upper respiratory tract (URT) and lower respiratory tract (LRT) of 77 patients was performed. A higher incidence of non-synonymous mutations and indels was observed in the LRT among minority variants. This might be explained by the ability of the virus to invade cells without interacting with ACE2 (e.g. exploiting macrophage phagocytosis). Minority variants are highly concentrated around the gene portion encoding for the Spike cleavage site, with a higher incidence in the URT; four mutations are highly recurring among samples and were found associated with the URT. Interestingly, 55.8% of minority variants detected in this locus were T>G and G>T transversions. Results from this study evidenced the presence of selective pressure and suggest that an evolutionary process is still ongoing in one of the crucial sites of spike protein associated with the spillover to humans.

A cross-sectional study of SARS-CoV-2 seropositivity among healthcare workers and residents of long-term facilities in Italy, January 2021

Long-term care facilities (LTCFs) are high-risk settings for SARS-CoV-2 infection. This study aimed to describe SARS-CoV-2 seropositivity among residents of LTCFs and health-care workers (HCWs). Subjects were recruited in January 2021 among unvaccinated HCWs of LTCFs and hospitals and residents of LTCFs in Northern Italy. Information concerning previous SARS-CoV-2 infections and a sample of peripheral blood were collected. Anti-S SARS-CoV-2 IgG antibodies were measured using the EUROIMMUN Anti-SARS-CoV-2 QuantiVac ELISA kit (EUROIMMUN Medizinische Labordiagnostika AG). For subjects with previous COVID-19 infection, gender, age, type of subject (HCW or resident), and time between last positive swab and blood draw were considered as possible determinants of two outcomes: the probability to obtain a positive serological result and antibody titer. Six hundred and fifty-eight subjects were enrolled. 56.1% of all subjects and 65% of residents presented positive results (overall median antibody titer: 31.0 RU/ml). Multivariable models identified a statistically significant 4% decrease in the estimated antibody level for each 30-day increase from the last positive swab. HCWs were associated with significant odds for seroreversion over time (OR: 0.926 for every 30 days, 95% CI: 0.860-0.998), contrary to residents (OR: 1.059, 95% CI: 0.919-1.22). Age and gender were not factors predicting seropositivity over time. Residents could have a higher probability of maintaining a seropositive status over time compared to HCWs.

Twelve Months with COVID-19: What Gastroenterologists Need to Know

Corona virus disease-19 (COVID-19) is the latest global pandemic. COVID-19 is mainly transmitted through respiratory droplets and, apart from respiratory symptoms, patients often present with gastrointestinal symptoms and liver involvement. Given the high percentage of COVID-19 patients that present with gastrointestinal symptoms (GIS), in this review, we report a practical up-to-date reference for the physician in their clinical practice with patients affected by chronic gastrointestinal (GI) diseases (inflammatory bowel disease, coeliac disease, chronic liver disease) at the time of COVID-19. First, we summarised data on the origin and pathogenetic mechanism of SARS-CoV-2. Then, we performed a literature search up to December 2020 examining clinical manifestations of GI involvement. Next, we illustrated and summarised the most recent guidelines on how to adhere to GI procedures (endoscopy, liver biopsy, faecal transplantation), maintaining social distance and how to deal with immunosuppressive treatment. Finally, we focussed on some special conditions such as faecal-oral transmission and gut microbiota. The rapid accumulation of information relating to this condition makes it particularly essential to revise the literature to take account of the most recent publications for medical consultation and patient care.

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

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

Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) has raised questions regarding vaccine protection against SARS-CoV-2 infection, transmission, and ongoing virus evolution. Twenty-three mildly symptomatic "vaccination breakthrough" infections were identified as early as January 2021 in Alachua County, Florida, among individuals fully vaccinated with either the BNT162b2 (Pfizer) or the Ad26 (Janssen/J&J) vaccines. SARS-CoV-2 genomes were successfully generated for 11 of the vaccine breakthroughs, and 878 individuals in the surrounding area and were included for reference-based phylogenetic investigation. These 11 individuals were characterized by infection with VOCs, but also low-frequency variants present within the surrounding population. Low-frequency mutations were observed, which have been more recently identified as mutations of interest owing to their location within targeted immune epitopes (P812L) and association with increased replicative capacity (L18F). We present these results to posit the nature of the efficacy of vaccines in reducing symptoms as both a blessing and a curse-as vaccination becomes more widespread and self-motivated testing reduced owing to the absence of severe symptoms, we face the challenge of early recognition of novel mutations of potential concern. This case study highlights the critical need for continued testing and monitoring of infection and transmission among individuals regardless of vaccination status.

Utilization of SARS-COV-2 positive donors and recipients for liver transplantation in the pandemic era - An evidence-based review

The current SARS-COV-2 pandemic led to a drastic drop in liver donation and transplantation in DDLT and LDLT settings. Living donations have decreased more than deceased organ donation due to the need to protect the interest of donors. In the SARS-COV-2 pandemic, major professional societies worldwide recommended against the use of organs from donors with acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. The basis for these recommendations are; SARS-CoV-2 could be transmitted to the recipient through organ transplantation and can result in severe manifestations; only limited effective targeted therapies are available, risk of transmission to the healthcare professionals, logistical limitations, and ethical concerns. In addition, end-stage liver disease patients on the waiting list represent vulnerable populations and are at higher risk for severe COVID-19 infection. Therefore, deferring life-saving transplants from COVID-positive donors during a pandemic may lead to more collateral damage by causing disease progression, increased death, and dropout from the waitlist. As this SARS-COV-2 pandemic is likely to stay with us for some time, we have to learn to co-exist with it. We believe that utilizing organs from mild/ asymptomatic COVID19 positive donors may expand the organ donor pool and mitigate disruptions in transplantation services during this pandemic.

Environmentally azithromycin pharmaceutical wastewater management and synergetic biocompatible approaches of loaded azithromycin@hematite nanoparticles

Pharmaceutical wastewater contamination via azithromycin antibiotic and the continuous emergence of some strains of bacteria, cancer, and the Covid-19 virus. Azithromycin wastewater treatment using the biosynthesized Hematite nanoparticles (α-HNPs) and the biocompatible activities of the resulted nanosystem were reported. Biofabrication of α-HNPs using Echinacea purpurea liquid extract as a previously reported approach was implemented. An evaluation of the adsorption technique via the biofabricated α-HNPs for the removal of the Azr drug contaminant from the pharmaceutical wastewater was conducted. Adsorption isotherm, kinetics, and thermodynamic parameters of the Azr on the α-HNPs surface have been investigated as a batch mode of equilibrium experiments. Antibacterial, anticancer, and antiviral activities were conducted as Azr@α-HNPs. The optimum conditions for the adsorption study were conducted as solution pH = 10, 150 mg dose of α-HNPs, and Azr concentration 400 mg/L at 293 K. The most fitted isothermal model was described according to the Langmuir model at adsorption capacity 114.05 mg/g in a pseudo-second-order kinetic mechanistic at R2 0.9999. Thermodynamic study manifested that the adsorption behavior is a spontaneous endothermic chemisorption process. Subsequently, studying the biocompatible applications of the Azr@α-HNPs. Azr@α-HNPs antibacterial activity revealed a synergistic effect in the case of Gram-positive more than Gram-negative bacteria. IC50 of Azr@α-HNPs cytotoxicity against MCF7, HepG2, and HCT116 cell lines was investigated and it was found to be 78.1, 81.7, and 93.4 µg/mL respectively. As the first investigation of the antiviral use of Azr@α-HNPs against SARS-CoV-2, it was achieved a safety therapeutic index equal to 25.4 revealing a promising antiviral activity. An admirable impact of the use of the biosynthesized α-HNPs and its removal nanosystem product Azr@α-HNPs was manifested and it may be used soon as a platform of the drug delivery nanosystem for the biomedical applications.

Early Treatment of High-Risk Hospitalized Coronavirus Disease 2019 (COVID-19) Patients With a Combination of Interferon Beta-1b and Remdesivir: A Phase 2 Open-label Randomized Controlled Trial

BACKGROUND

Early antiviral therapy was effective in the treatment of coronavirus disease 2019 (COVID-19). We assessed the efficacy and safety of combined interferon beta-1b and remdesivir treatment in hospitalized COVID-19 patients.

METHODS

We conducted a multicentre, prospective open-label, randomized-controlled trial involving high-risk adults hospitalized for COVID-19. Patients were randomly assigned to a 5-day interferon beta-1b 16 million units daily and remdesivir 200 mg loading on day 1 followed by 100 mg daily on day 2 to 5 (combination group), or to remdesivir only of similar regimen (control group) (1:1). The primary endpoint was the time to complete alleviation of symptoms (NEWS2 = 0).

RESULTS

Two-hundred and twelve patients were enrolled. The median days of starting treatment from symptom onset was 3 days. The median age was 65 years, and 159 patients (75%) had chronic disease. The baseline demographics were similar. There was no mortality. For the primary endpoint, the combination group was significantly quicker to NEWS2 = 0 (4 vs 6.5 days; hazard ratio [HR], 6.59; 95% confidence interval [CI], 6.1-7.09; P < .0001) when compared to the control group. For the secondary endpoints, the combination group was quicker to negative nasopharyngeal swab (NPS) viral load (VL) (6 vs 8 days; HR, 8.16; 95% CI, 7.79-8.52; P < .0001) and to develop seropositive immunoglobulin G (IgG) (8 vs 10 days; HR, 10.78; 95% CI, 9.98-11.58; P < .0001). All adverse events resolved upon follow-up. Combination group (HR, 4.1 95% CI, 1.9-8.6, P < .0001) was the most significant independent factor associated with NEWS2 = 0 on day 4.

CONCLUSIONS

Early treatment with interferon beta-1b and remdesivir was safe and better than remdesivir only in alleviating symptoms, and in shortening viral shedding and hospitalization with earlier seropositivity in high-risk COVID-19 patients.

CLINICAL TRIALS REGISTRATION

NCT04647695.

COVID-19 Mortality and Therapeutics in Nebraska and Southwest Iowa during Early Pandemic

Different pharmacotherapeutics have been introduced, and then stopped or continued, for the treatment of SARS-CoV-2. We evaluated the risks associated with mortality from SARS-CoV-2 infection. METHODS: Data was concurrently or retrospectively captured on COVID-19 hospitalized patients from 6 regional hospitals within the health system. Demographic details, the source of SARS-CoV-2 infection, concomitant disease status, as well as the therapeutic agents used for treating SARS-CoV-2 (e.g., antimicrobials, dexamethasone, convalescent plasma, tocilizumab, and remdesivir) were recorded. Discrete and continuous variables were analyzed using SPSS (ver. 27). Logistic regression identified variables significantly correlated with mortality. RESULTS: 471 patients (admitted from 1 March 2020 through 15 July 2020) were reviewed. Mean (±SD) age and body weight (kg) were 62.5 ± 17.7 years and 86.3 ± 27.1 kg, respectively. Patients were Caucasian (50%), Hispanic (34%), African-American (10%), or Asian (5%). Females accounted for 52% of patients. Therapeutic modalities used for COVID-19 illness included remdesivir (16%), dexamethasone (35%), convalescent plasma (17.8%), and tocilizumab (5.8%). The majority of patients returned home (62%) or were transferred to a skilled nursing facility (23%). The overall mortality from SARS-CoV-2 was 14%. Logistic regression identified variables significantly correlated with mortality. Intubation, receipt of dexamethasone, African-American or Asian ethnicity, and being a patient from a nursing home were significantly associated with mortality (x2 = 86.36 (13) p < 0.0005). CONCLUSIONS: SARS-CoV-2 infected hospitalized patients had significant mortality risk if they were intubated, received dexamethasone, were of African-American or Asian ethnicity, or occupied a nursing home bed prior to hospital admission.

Contribution of low population immunity to the severe Omicron BA.2 outbreak in Hong Kong

Monitoring population protective immunity against SARS-CoV-2 variants is critical for risk assessment. We hypothesize that Hong Kong's explosive Omicron BA.2 outbreak in early 2022 could be explained by low herd immunity. Our seroprevalence study using sera collected from January to December 2021 shows a very low prevalence of neutralizing antibodies (NAb) against ancestral virus among older adults. The age group-specific prevalence of NAb generally correlates with the vaccination uptake rate, but older adults have a much lower NAb seropositive rate than vaccination uptake rate. For all age groups, the seroprevalence of NAb against Omicron variant is much lower than that against the ancestral virus. Our study suggests that this BA.2 outbreak and the exceptionally high case-fatality rate in the ≥80 year-old age group (9.2%) could be attributed to the lack of protective immunity in the population, especially among the vulnerable older adults, and that ongoing sero-surveillance is essential.

Positivity rates of SAR-CoV-2 infection in orthodontic patients at the orthodontic clinic, University of Illinois Chicago

COVID-19 has impacted and increased risks for healthcare providers, including orthodontists. There is no information regarding the potential transmission risks in the orthodontic community. This study aims to compare the positivity rate of SARS-CoV-2 infection in orthodontic patients at the University of Illinois Chicago (UIC) orthodontic clinic to the positivity rate of the local population in Chicago. All orthodontic patients who sought treatment at the UIC orthodontic clinic from June 16 to October 31, 2021, were invited to participate in the study. Three milliliters of saliva from the participants were collected in the sample collection tubes and subjected to a polymerase chain reaction (PCR) based assay to detect SAR-CoV-2. All participants’ age, sex, history of COVID-19 infection, and vaccination status were recorded. The COVID-19 positivity rates of Chicago, Cook County of Illinois, and the orthodontic clinic at UIC were compared. One thousand four hundred and thirty-seven orthodontic patients aged 6 to 70 years old (41.8% males and 58.2% females) participated in the study. Among all participants, nine participants tested positive for SARS-CoV-2 (5 males and 4 females). During the study, the average COVID-19 positivity rate at the UIC orthodontic clinic was 0.626%. All of the positive participants were asymptomatic, and two of the participants had a history of COVID-19 infection. Among all positive participants, three participants had received complete COVID-19 vaccination. An increased frequency of positive cases at the orthodontic clinic was observed during the time of high positivity rate in Chicago and Cook County. A potential risk of COVID-19 transmission from patients to orthodontic providers remains, even with asymptomatic and vaccinated patients.

Prognostic Value of SARS-CoV-2 Anti-RBD IgG Antibody Quantitation on Clinical Outcomes in Hospitalized COVID-19 Patients

Background

Antibody levels against SARS-CoV-2 can be used as an indicator of recent or past vaccination or infection. However, the prognostic value of antibodies targeting the receptor binding protein (anti-RBD) in hospitalized patients is not widely reported.

Purpose

Determine prognostic impact of SARS-CoV-2 antibody quantification at the time of admission on clinical outcomes in hospitalized COVID-19 patients.

Methods

We conducted a pilot observational study on patients hospitalized with SARS-CoV-2 infection to determine the prognostic impact of antibody quantitation within the first two days of admission. Anti-nucleocapsid IgG (anti-N) and Anti-RBD levels were measured. Anti-RBD level of 500 AU/mL was used as a cutoff to stratify patients. Spearman's rank Coefficient (rs) was used to demonstrate association.

Results

Of the 26 patients included, those who were vaccinated more frequently tested positive for Anti-RBD (100% vs 46.2%, P = 0.005) with higher median titer level (623 vs 0, P = 0.011) compared to unvaccinated patients. Anti-N positivity was more frequently seen in unvaccinated patients (53.9% vs 7.7%, P = 0.03). Anti-RBD levels >500 were associated with lower overall hospital length of stay (LOS)(5 vs 10 days, P = 0.046). The analysis employing a Spearman Rank coefficient demonstrated a strong negative correlation between anti-S titer and LOS (rs=-.515, p = 0.007) and a moderate negative correlation with oxygen needs (rs =-.401, p = 0.042).

Conclusion

Anti-RBD IgG levels were associated with lower LOS and oxygen needs during hospitalization. Further studies are needed to determine if levels on admission can be used as a prognostic indicator.

Uncertainty analysis of facemasks in mitigating SARS-CoV-2 transmission

In the context of global spread of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2), there is a controversial issue on whether the use of facemasks is promising to control or mitigate the COVID-19 transmission. This study modeled the SARS-CoV-2 transmission process and analyzed the ability of surgical mask and N95 in reducing the infection risk with Sobol's analysis. Two documented outbreaks of COVID-19 with no involvers wearing face masks were reviewed in a restaurant in Guangzhou (China) and a choir rehearsal in Mount Vernon (USA), suggesting that the proposed model can be well validated when airborne transmission is assumed to dominate the virus transmission indoors. Subsequently, the uncertainty analysis of the protection efficiency of N95 and surgical mask were conducted with Monte Carlo simulations, with three main findings: (1) the uncertainty in infection risk is primarily apportioned by respiratory activities, virus dynamics, environment factors and individual exposures; (2) wearing masks can effectively reduce the SARS-CoV-2 infection risk to an acceptable level (< 10^-3) by at least two orders of magnitude; (3) faceseal leakage can reduce protection efficiency by approximately 4% when the infector is speaking or coughing, and by approximately 28% when the infector is sneezing. This work indicates the effectiveness of non-pharmaceutical interventions during the pandemic, and implies the importance of the synergistic studies of medicine, environment, social policies and strategies, etc., on reducing hazards and risks of the pandemic.

Development of novel spectroscopic and machine learning methods for the measurement of periodic changes in COVID-19 antibody level

In this research, blood samples of 47 patients infected by COVID were analyzed. The samples were taken on the 1st, 3rd and 6th month after the detection of COVID infection. Total antibody levels were measured against the SARS-CoV-2 N antigen and surrogate virus neutralization by serological methods. To differentiate COVID patients with different antibody levels, Fourier Transform InfraRed (FTIR) and Raman spectroscopy methods were used. The spectroscopy data were analyzed by multivariate analysis, machine learning and neural network methods. It was shown, that analysis of serum using the above-mentioned spectroscopy methods allows to differentiate antibody levels between 1 and 6 months via spectral biomarkers of amides II and I. Moreover, multivariate analysis showed, that using Raman spectroscopy in the range between 1317 cm-1 and 1432 cm-1, 2840 cm-1 and 2956 cm-1 it is possible to distinguish patients after 1, 3, and 6 months from COVID with a sensitivity close to 100%.

Case Report: Assessing COVID-19 Transmission in Professional Volleyball in Germany, September to December 2020: An Epidemiological Study

Introduction

The SARS-CoV-2 pandemic poses extraordinary challenges in all fields of daily life. The WHO recommended social distancing guidelines and person-to-person contact was strongly discouraged to contain transmission. Team-based sports were questioned and widely debated. However, there is a lack of available evidence on the risk of in-game SARS-CoV-2 transmission. We aim to derive new insights regarding the risk of SARS-CoV2 infection during team sports and provide current opinion on how to behave during training and competition.

Methods

We report on six competitive male volleyball players (national level) of the same team who were infected with COVID-19. The mode of transmission and potential virus spreading within the team was investigated. The entire course of infection was documented by detailed medical history of the players and RT-PCR tests confirmed suspected infections. Serological testing was performed to establish the antibody status of the team.

Results

The investigation did not show strong evidence of viral transmission within the team during sporting activities. Only two players with PCR-proven infection hat detectable antibodies in two antibody assays.

Conclusion

Private and social gatherings can spread infection into team sports. Clearly defined test strategies and strict adherence to standard COVID-19 hygiene guidelines during sports seasons cannot be overemphasized.

Is Lipid Specificity Key to the Potential Antiviral Activity of Mouthwash Reagent Chlorhexidine against SARS-CoV-2?

Chlorhexidine (CHX), a popular antibacterial drug, is widely used for oral health. Emerging pieces of evidence suggest that commercially available chlorhexidine mouthwash formulations are effective in suppressing the spread of SARS-CoV-2, possibly through destabilization of the viral lipid envelope. CHX is known for its membrane-active properties; however, the molecular mechanism revealing how it damages the viral lipid envelope is yet to be understood. Here we used extensive conventional and umbrella sampling simulations to quantify the effects of CHX on model membranes mimicking the composition of the SARS-CoV-2 outer lipid membrane as well as the host plasma membrane. Our results show that the lipid composition and physical properties of the membrane play an important role in binding and insertion, with CHX binding favorably to the viral membrane over the plasma membrane. Among the simulated lipids, CHX preferentially binds to anionic lipids, PS and PI, which are more concentrated in the viral membrane. The deeper and stable binding of CHX to the viral membrane results in more pronounced swelling of the membrane laterally with a thinning of the bilayer. The overall free energies of pore formation are strongly reduced for the viral membrane compared to the plasma membrane; however, CHX has a larger concentration-dependent effect on free energies of pore formation in the plasma membrane than the viral membrane. The results indicate that CHX is less toxic to the human plasma membrane at low concentrations. Our simulations reveal that CHX facilitates pore formation by the combination of thinning the membrane and accumulation at the water defect. This study provides insights into the mechanism underlying the anti-SARS-CoV-2 potency of CHX, supporting its potential for application as an effective and safe oral rinse agent for preventing viral transmission.

Advancements in Testing Strategies for COVID-19

The SARS-CoV-2 coronavirus, also known as the disease-causing agent for COVID-19, is a virulent pathogen that may infect people and certain animals. The global spread of COVID-19 and its emerging variation necessitates the development of rapid, reliable, simple, and low-cost diagnostic tools. Many methodologies and devices have been developed for the highly sensitive, selective, cost-effective, and rapid diagnosis of COVID-19. This review organizes the diagnosis platforms into four groups: imaging, molecular-based detection, serological testing, and biosensors. Each platform's principle, advancement, utilization, and challenges for monitoring SARS-CoV-2 are discussed in detail. In addition, an overview of the impact of variants on detection, commercially available kits, and readout signal analysis has been presented. This review will expand our understanding of developing advanced diagnostic approaches to evolve into susceptible, precise, and reproducible technologies to combat any future outbreak.

The Pre-Vaccination Donated Blood Is Free from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) but Is Rich with Anti-SARS-CoV-2 Antibodies: A Cross-Section Saudi Study

(1) Backgrounds and Objectives: Since its discovery, information about the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has spread rapidly. However, many issues remain unresolved. Coronaviruses are primarily transmitted through respiratory secretions. The possibility of transmission via donated blood transfusion deserves studying. This is the first study in Saudi Arabia to look at pre-vaccination donated blood anti-SARS-CoV-2 antibody content as a marker for virus transmission via viral RNA positive blood and/or the potential therapeutic value of convalescent plasma. (2) Methods: A total of 300 blood samples were sequentially collected from unvaccinated donors who donated blood to the blood bank of Prince Mutaib Bin Abdulaziz Hospital in Sakaka, Al-Jouf, Saudi Arabia. Specific ELISA was used to detect anti-SARS-CoV-2 IgG and IgM antibodies. SARS-CoV-2 was detected using specific real-time reverse-transcription PCR (rRT-PCR). (3) Results: The prevalence of anti-SARS-CoV-2 IgG was low (9%), whereas the prevalence of anti-SARS-CoV-2 IgM was high (65%). Relevant demographics, anthropometrics, and lifestyle factors revealed significant associations (p < 0.05) between IgM-positivity only vs. age (age group 21−30 years), postgraduate education, no history of international travel, IgG-negativity, and absence of experience with COVID-19-like symptoms. Furthermore, there are significant associations (p < 0.05) between IgG-positivity only vs. age (age group 21−30 years), postgraduate education, and being a non-healthcare worker. All donors in the anti-SARS-CoV-2 IgG-positive group (n = 27) had previously experienced symptoms similar to COVID-19 (p < 0.001) and most of them (n = 24) showed anti-SARS-CoV-2 IgM-positive test (p = 0.006). However, all the samples tested negative for SARS-CoV-2 RNA using rRT-PCR. (4) Conclusion: Our findings add to the growing body of evidence that donated blood is safe, with the added benefit of convalescent plasma rich in potentially neutralizing IgG and IgM against SARS-CoV-2.

An impedimetric biosensor for COVID-19 serology test and modification of sensor performance via dielectrophoresis force

Coronavirus disease 2019 (COVID-19) has caused significant global morbidity and mortality. The serology test that detects antibodies against the disease causative agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has often neglected value in supporting immunization policies and therapeutic decision-making. The ELISA-based antibody test is time-consuming and bulky. This work described a gold micro-interdigitated electrodes (IDE) biosensor for COVID antibody detection based on Electrochemical Impedance Spectroscopy (EIS) responses. The IDE architecture allows easy surface modification with the viral structure protein, Spike (S) protein, in the gap of the electrode digits to selectively capture anti-S antibodies in buffer solutions or human sera. Two strategies were employed to resolve the low sensitivity issue of non-faradic impedimetric sensors and the sensor fouling phenomenon when using the serum. One uses secondary antibody-gold nanoparticle (AuNP) conjugates to further distinguish anti-S antibodies from the non-specific binding and obtain a more significant impedance change. The second strategy consists of increasing the concentration of target antibodies in the gap of IDEs by inducing an AC electrokinetic effect such as dielectrophoresis (DEP). AuNP and DEP methods reached a limit of detection of 200 ng/mL and 2 μg/mL, respectively using purified antibodies in buffer, while the DEP method achieved a faster testing time of only 30 min. Both strategies could qualitatively distinguish COVID-19 antibody-positive and -negative sera. Our work, especially the impedimetric detection of COVID-19 antibodies under the assistance of the DEP force presents a promising path toward rapid, point-of-care solutions for COVID-19 serology tests.

Head-to-Head Comparison of 5 Anti-SARS-CoV-2 Assays Performance in One Hundred COVID-19 Vaccinees, over an 8-Month Course

The immunoassays used to measure anti-spike SARS-CoV-2 antibodies are widely available on the market. However, their performance in COVID-19 vaccinees is not yet adequately assessed. Our study provides a head-to-head comparison of five methods: Abbott's S1-RBD IgG, Roche's S1-RBD total antibody, Euroimmun's S1 IgG, and DiaSorin's TrimericS IgG and S1/S2 IgG assays. Testing was performed in one hundred vaccinated subjects, at eight timepoints over eight months after vaccination. The results differed substantially between methods; however, they correlated strongly and demonstrated the individuals' responses to both doses of vaccination and the waning of humoral immunity after eight months. Importantly, we encountered a high percentage of results above the assay-specific upper quantitation limit (UQL) for undiluted samples. This was the most pronounced for the Roche's and Euroimmun's assays. The Abbott's assay showed the lowest percentage of results above the UQL. We also attempted to find a common way to establish antibody concentrations that might be classified as high. However, this resulted in between 10% and 100% of such results for different methods on day 240'. This highlights the need for an assay-specific approach for adjusting the cut-offs that may indicate COVID-19 immunity.

Rapid, adaptable and sensitive Cas13-based COVID-19 diagnostics using ADESSO

During the ongoing COVID-19 pandemic, PCR testing and antigen tests have proven critical for helping to stem the spread of its causative agent, SARS-CoV-2. However, these methods suffer from either general applicability and/or sensitivity. Moreover, the emergence of variant strains creates the need for flexibility to correctly and efficiently diagnose the presence of substrains. To address these needs we developed the diagnostic test ADESSO (Accurate Detection of Evolving SARS-CoV-2 through SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) Optimization) which employs Cas13 to diagnose patients in 1 h without sophisticated equipment. Using an extensive panel of clinical samples, we demonstrate that ADESSO correctly identifies infected individuals at a sensitivity and specificity comparable to RT-qPCR on extracted RNA and higher than antigen tests for unextracted samples. Altogether, ADESSO is a fast, sensitive and cheap method that can be applied in a point of care setting to diagnose COVID-19 and can be quickly adjusted to detect new variants.

Accurate virus identification with interpretable Raman signatures by machine learning

Significance A large Raman dataset collected on a variety of viruses enables the training of machine learning (ML) models capable of highly accurate and sensitive virus identification. The trained ML models can then be integrated with a portable device to provide real-time virus detection and identification capability. We validate this conceptual framework by presenting highly accurate virus type and subtype identification results using a convolutional neural network to classify Raman spectra of viruses. The accurate and interpretable ML model developed for Raman virus identification presents promising potential in a real-time, label-free virus detection system that could be used in future outbreaks and pandemics.

Evaluation of real-time NASBA assay for the detection of SARS-CoV-2 compared with real-time PCR

Purpose

In January 2020, the COVID-19 pandemic started and has severely affected all countries around the world. The clinical symptoms alone are not sufficient for a proper diagnosis. Thus, molecular tests are required. Various institutes and researchers developed real-time PCR-based methods for the detection of the virus. However, the method needs expensive equipment. In the present study, we developed a real-time NASBA assay for the detection of SARS-CoV-2.

Methods

Primers and molecular beacon probes for RdRp and N genes were designed. In silico analysis showed that primers and the probes were specific for SARS-CoV-2. The standard samples with known copy numbers of the virus were tested using the NASBA assay and an FDA-approved real-time PCR kit. A series of standard samples were prepared and tested. Clinical sensitivity, precision analysis, and clinical assessment of the assay were performed.

Results

The limit of detection of the assay was 200 copies/mL. The clinical sensitivity of the assay was 97.64%. The intra-assay and inter-assay for both N and RdRp genes were less than 5% and 10%, respectively. Clinical assessment of the assay showed that the positive agreement rate and negative agreement rate of the assays were determined to be 97.64% and 100%, respectively.

Conclusions

The results of the present study show that the developed real-time NASBA is a sensitive and specific method for the detection of SARS-CoV-2 and is comparable with real-time PCR. NASBA is an isothermal signal amplification method, and if stand-alone fluorescent readers are available, the real-time NASBA can be used without the need for expensive thermocyclers. In addition compared to other isothermal methods like LAMP, the primer design is straightforward. Thus, real-time NASBA could be a suitable method for inexpensive SARS-CoV-2 detection.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s11845-022-03046-2.

Multicompartmental Mathematical Model of SARS-CoV-2 Distribution in Human Organs and Their Treatment

Patients with COVID-19 can develop pneumonia, severe symptoms of acute respiratory distress syndrome, and multiple organ failure. Nevertheless, the variety of forms of this disease requires further research on the pathogenesis of this disease. Based on the analysis of published data and original experiments on the concentrations of SARS-CoV-2 in biological fluids of the nasopharynx, lungs, and intestines and using a developed modular model of the virus distribution in human tissue and organs, an assessment of the SARS-CoV-2 reproduction in various compartments of the body is presented. Most of the viral particles can transport to the esophagus from the nasopharynx. The viral particles entering the gastrointestinal tract will obviously be accompanied by the infection of the intestinal epithelium and accumulation of the virus in the intestinal lumen in an amount proportional to their secretory and protein-synthetic activities. The relatively low concentration of SARS-CoV-2 in tissues implies an essential role of transport processes and redistribution of the virus from the nasopharynx and intestines to the lungs. The model simulations also suppose that sanitation of the nasopharynx mucosa at the initial stage of the infectious process has prospects for the use in medical practice.

Microfluidic particle dam for direct visualization of SARS-CoV-2 antibody levels in COVID-19 vaccinees

Various COVID-19 vaccines are currently deployed, but their immunization varies and decays with time. Antibody level is a potent correlate to immune protection, but its quantitation relies on intensive laboratory techniques. Here, we report a decentralized, instrument-free microfluidic device that directly visualizes SARS-CoV-2 antibody levels. Magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) can bind to SARS-CoV-2 antibodies simultaneously. In a microfluidic chip, this binding reduces the incidence of free PMPs escaping from magnetic separation and shortens PMP accumulation length at a particle dam. This visual quantitative result enables use in either sensitive mode [limit of detection (LOD): 13.3 ng/ml; sample-to-answer time: 70 min] or rapid mode (LOD: 57.8 ng/ml; sample-to-answer time: 20 min) and closely agrees with the gold standard enzyme-linked immunosorbent assay. Trials on 91 vaccinees revealed higher antibody levels in mRNA vaccinees than in inactivated vaccinees and their decay in 45 days, demonstrating the need for point-of-care devices to monitor immune protection.

Prevalence of SARS-CoV-2 antibodies and risk factors in the pandemic epicentre of Catalonia

To define the seroprevalence of antibodies against SARS-CoV-2 in the municipality of Vilanova del Camí (in the region of Conca d'Ódena, Barcelona, Spain) and to know the risk factors associated with positive seroprevalence. Cross-sectional descriptive study. The population of Vilanova del Camí had the opportunity to voluntarily attend two screenings (October and December 2020) for antibodies against the nucleocapsid protein of SARS-CoV-2 using a Rapid Diagnostic Test (RDT) (Salocor (Salofa Oy). Participants in the screening signed an informed consent form. From the 3,610 attendees at the screening, 2,170 patients were randomly selected. The relationship between antibody test results and other demographic (sex, age, morbidity index) and clinical (diagnoses, smoking and drugs) variables was analysed. The prevalence of antibodies against SARS-CoV-2 was 9.6% (95% CI of 8.4% to 10.9%) and was similar for men and women but increased with age. Among complex chronic patients, 14.3% had antibodies against SARS-CoV-2, and among patients with advanced chronic disease, 25% had antibodies against SARS-CoV-2. Age, AMG (Adjusted Morbidity Groups) index, COVID-19 diagnosis and contact with a COVID-19 case were risk factors for positive seroprevalence. A higher seroprevalence was detected in the October screening (12.16%) than in the December screening (8.38%). In the December screening, obesity was a risk factor for positive seroprevalence. This study demonstrates the high seroprevalence of antibodies against SARS-CoV-2 in the pandemic epicentre of Catalonia.

Numerical evaluation of face masks for prevention of COVID-19 airborne transmission

The COVID-19 pandemic has forced governments around the globe to apply various preventive measures for public health. One of the most effective measures is wearing face masks, which plays a vital role in blocking the transmission of droplets and aerosols. To understand the protective mechanism of face masks, especially in indoor environments, we apply a computational fluid dynamics technique to predict the lifetime of cough droplets. Therefore, we can assess the exposure risk in a ventilated room where an infected individual wears a face mask or not. We focus on the dynamic evaporation and diffusion of droplets in a human-cough process, which is a major cause for the spread of the virus. We find that wearing a face mask can effectively reduce the total mass and Sauter mean diameter of the residual droplets after a single cough. The mass concentration of virus-carrying droplets in the ventilated room decreases by 201, 43,786, and 307,060 times, corresponding to wearing cotton face masks, surgical face masks, and N95 face masks, respectively. However, the maximum travel distance of 80% droplets is insensitive to wearing a face mask or not. Therefore, the residual droplets are widely distributed due to the influence of indoor airflow. Furthermore, we study aerosol exposure risks in different areas of the room and find that high concentrations of aerosols occur in the streamline through an infected individual, especially next to the individual within 1.5 m. This strongly suggests a social distance despite the fact that the majority of droplets are filtered by face masks. This study explains the impact of face masks and airflow on indoor exposure risks and further inspires potential measures for public health, for example, no individuals should sit near the air supply opening.

COVID-19 hastalarının semptomlarına ve pnömoni varlığına göre antikor tepkileri

Introduction: The aim of the study was to examine the 30-day total SARS-CoV-2 antibody positivity in patients across a clinical spectrum ranging from asymptomatic to pneumonia.Methods: This prospective cohort study consisted of 51 consecutive patients who were RT-PCR positive and diagnosed COVID-19 pneumonia (Group 1) and 58 consecutive patients who were also RT-PCR positive but were asymptomatic or had mild symptoms (Group 2). On the 30th day from the date of symptom onset, the patients were called for examination and blood samples were taken for the detection of SARS-CoV-2 antibodies.Results: Patients with pneumonia, fever, muscle pain, and loss of taste and smell had significantly higher rates of antibody positivity (p= 0.001, 0.003, 0.030, and 0.018, respectively). Antibody positivity was found to be significantly higher in patients with at least one symptom on admission compared to asymptomatic patients (p = 0.001). While the antibody positivity rate was 96.1% in Group 1 (patients with pneumonia), it was 50% in Group 2 (patients without pneumonia), and 77.7% in patients with at least one symptom on admission compared to 33.3% in asymptomatic patients (p=0.001).Conclusions: Patients with COVID-19 pneumonia have significantly higher disease-specific total antibody positivity rates than patients without pneumonia. Considering the 50% antibody positivity in patients who had COVID-19 infection who were asymptomatic or had symptoms other than pneumonia, the issue of COVID-19 re-infection and immunity is much more important than it appears. 

SARS-CoV-2 RNA copy number is a factor associated with the mortality of COVID-19 and improves the predictive performance of mortality in severe cases

Factors associated with mortality are important for the treatment of coronavirus disease 2019 (COVID-19). The polymerase chain reaction (PCR) test is the gold standard for diagnosing COVID-19 and reflects the viral load in the upper respiratory tract. This study enrolled 523 patients. Four hundred forty-one and 75 patients were performed PCR testing in nasopharyngeal swabs and sputum specimens, respectively, within 20 days from the onset. We investigated the association between RNA copy number and the severity and mortality of COVID-19, and its effect on the predictive performance for the severity and mortality. RNA copy numbers in nasopharyngeal swabs were higher in the non-survivor group than in the survivor group. Multivariate logistic regression analysis identified that the high RNA copy number (≥ 9 log₁₀ /swab) in nasopharyngeal swabs was a factor associated with mortality (odds ratio, 4.50; 95% confidence interval, 1.510 - 13.100; p = 0.008). Furthermore, in severe cases, adding RNA copy number (≥ 9 log₁₀ /swab), which was adjusted by duration from onset to PCR, improved mortality predictive performance based on known factors. The RNA copy number is a factor associated with the mortality of COVID-19 and can improve the predictive performance of mortality in severe cases.

Decreased Antibiotic Consumption Coincided with Reduction in Bacteremia Caused by Bacterial Species with Respiratory Transmission Potential during the COVID-19 Pandemic

Nonpharmaceutical interventions implemented during the COVID-19 pandemic (2020−2021) have provided a unique opportunity to understand their impact on the wholesale supply of antibiotics and incidences of infections represented by bacteremia due to common bacterial species in Hong Kong. The wholesale antibiotic supply data (surrogate indicator of antibiotic consumption) and notifications of scarlet fever, chickenpox, and tuberculosis collected by the Centre for Health Protection, and the data of blood cultures of patients admitted to public hospitals in Hong Kong collected by the Hospital Authority for the last 10 years, were tabulated and analyzed. A reduction in the wholesale supply of antibiotics was observed. This decrease coincided with a significant reduction in the incidence of community-onset bacteremia due to Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis, which are encapsulated bacteria with respiratory transmission potential. This reduction was sustained during two pandemic years (period 2: 2020−2021), compared with eight pre-pandemic years (period 1: 2012−2019). Although the mean number of patient admissions per year (1,704,079 vs. 1,702,484, p = 0.985) and blood culture requests per 1000 patient admissions (149.0 vs. 158.3, p = 0.132) were not significantly different between periods 1 and 2, a significant reduction in community-onset bacteremia due to encapsulated bacteria was observed in terms of the mean number of episodes per year (257 vs. 58, p < 0.001), episodes per 100,000 admissions (15.1 vs. 3.4, p < 0.001), and per 10,000 blood culture requests (10.1 vs. 2.1, p < 0.001), out of 17,037,598 episodes of patient admissions with 2,570,164 blood culture requests. Consistent with the findings of bacteremia, a reduction in case notification of scarlet fever and airborne infections, including tuberculosis and chickenpox, was also observed; however, there was no reduction in the incidence of hospital-onset bacteremia due to Staphylococcus aureus or Escherichia coli. Sustained implementation of non-pharmaceutical interventions against respiratory microbes may reduce the overall consumption of antibiotics, which may have a consequential impact on antimicrobial resistance. Rebound of conventional respiratory microbial infections is likely with the relaxation of these interventions.

A paper-based optical sensor for the screening of viruses through the cysteine residues of their surface proteins: A proof of concept on the detection of coronavirus infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to human health. Current methods such as reverse transcription polymerase chain reaction (qRT-PCR) are complex, expensive, and time-consuming. Rapid, and simple screening methods for the detection of SARS-CoV-2 are critically required to fight the current pandemic. In this work we present a proof of concept for, a simple optical sensing method for the screening of SARS-CoV-2 through its spike protein subunit S1. The method utilizes a target-specific extractor chip to bind the protein from the biological specimens. The disulfide bonds of the protein are then reduced into a biothiol with sulfhydryl (SH) groups that react with a blue-colored benzothiazole azo dye-Hg complex (BAN-Hg) and causes the spontaneous change of its blue color to pink which is observable by the naked eye. A linear relationship between the intensity of the pink color and the logarithm of reduced S1 protein concentration was found within the working range 130 ng.mL⁻¹-1.3 pg mL⁻¹. The lowest limit of detection (LOD) of the assay was 130 fg mL⁻¹. A paper based optical sensor was fabricated by loading the BAN-Hg sensor onto filter paper and used to screen the S1 protein in spiked saliva and patients’ nasopharyngeal swabs. The results obtained by the paper sensor corroborated with those obtained by qRT-PCR. The new paper-based sensing method can be extended to the screening of many viruses (e.g. the human immunodeficiency virus, the human polyomavirus, the human papilloma virus, the adeno associated viruses, the enteroviruses) through the cysteine residues of their capsid proteins. The new method has strong potential for screening viruses at pathology labs and in remote areas that lacks advanced scientific infrastructure. Further clinical studies are warranted to validate the new sensing method.

Highly sensitive electrochemical aptasensor for SARS-CoV-2 antigen detection based on aptamer-binding induced multiple hairpin assembly signal amplification

In this work, a brief electrochemical aptasensor was developed for highly sensitive detection of SARS-CoV-2 antigen utilizing an aptamer-binding induced multiple hairpin assembly strategy for signal amplification. In the presence of SARS-CoV-2, a pair of aptamers was brought in a close proximity according to the aptamer-protein antigen binding, which initiated strand displacement reaction thereby triggering a multiple hairpin assembly to obtain long linear DNA concatemers on the electrode surface. As the fabricated hairpin probes were labeled with biotin, massive streptavidin-alkaline phosphatases (ST-ALP) could be further introduced on the electrode interface via biotin-streptavidin interaction thus generating strong electrochemical signal in electrolyte solution containing 1-naphthol phosphate. Benefiting from the non-enzymatic multiple hairpin assembly signal amplification strategy, the designed aptasensor for SARS-CoV-2 spike protein detection exhibited the wide linear range from 50 fg·mL⁻¹ to 50 ng·mL⁻¹ and low detection limit of 9.79 fg·mL⁻¹. Meaningfully, this proposed electrochemical assay provided a potential application for the point of care analysis of viral diseases under ambient temperature.

Factors Associated with Prolonged RT-PCR SARS-CoV-2 Positive Testing in Patients with Mild and Moderate Forms of COVID-19: A Retrospective Study

Background and objectives: This article aims to evaluate the number of days necessary for patients with mild and moderate forms of COVID-19 to reach undetectable levels of SARS-CoV-2 RNA in the upper respiratory tract specimens. As a secondary objective, we sought to establish a correlation between different conditions associated with longer viral load as this could result in a longer period of contagion and infectivity. Materials and Methods: It is a retrospective study. A total of 70 patients with confirmed mild and moderate forms of COVID-19 were enrolled in our study. Results: Number of days with traceable viral load was 25.93 (±6.02) days in patients with mild COVID-19 and 26.97 (±8.30) in moderate form (p = 0.72). Age, male gender, and obesity, along with several chronic conditions (cardiac, liver, renal, and neurological disease), were associated with prolonged positive RT-PCR test from the nasal swab (therefore prolonged viral load). These are in general, risk factors for severe forms of COVID-19. Conclusions: There are several conditions associated with prolonged positive RT-PCR in mild and moderate forms of COVID-19. As to why and what is the significance of it remains to be studied.

Numerical Flow Simulation on the Virus Spread of SARS-CoV-2 Due to Airborne Transmission in a Classroom

In order to continue using highly frequented rooms such as classrooms, seminar rooms, offices, etc., any SARS-CoV-2 virus concentration that may be present must be kept low or reduced through suitable ventilation measures. In this work, computational fluid dynamics (CFD) is used to develop a virtual simulation model for calculating and analysing the viral load due to airborne transmission in indoor environments aiming to provide a temporally and spatially-resolved risk assessment with explicit relation to the infectivity of SARS-CoV-2. In this work, the first results of the model and method are presented. In particular, the work focuses on a critical area of the education infrastructure that has suffered severely from the pandemic: classrooms. In two representative classroom scenarios (teaching and examination), the duration of stay for low risk of infection is investigated at different positions in the rooms for the case that one infectious person is present. The results qualitatively agree well with a documented outbreak in an elementary school but also show, in comparisons with other published data, how sensitive the assessment of the infection risk is to the amount of virus emitted on the individual amount of virus required for infection, as well as on the supply air volume. In this regard, the developed simulation model can be used as a useful virtual assessment for a detailed seat-related overview of the risk of infection, which is a significant advantage over established analytical models.

SARS-CoV-2 genomic surveillance as an evidence-based infection control approach in an offshore petroleum employee population

BACKGROUND

Industrial hygienists (IH) in the oil and gas business instituted an extraordinary number of safety protocols to limit spread of SARS-CoV-2 onto offshore platforms in the Gulf of Mexico. We used genomic surveillance to provide actionable information concerning the efficacy of their efforts.

METHODS

Over 6 months, employees at a single company were serology and PCR tested during a 1-5 day predeployment quarantine and when postdeployment symptoms were reported. From each positive test (n = 49), SARS-CoV-2 genomes were sequenced. Phylogenetic analysis was used to investigate the epidemiology of transmissions.

RESULTS

Genomic surveillance confirmed 2 viral strains were infecting 18 offshore workers. Genomic data combined with epidemiological data suggested that a change in quarantine protocols contributed to these outbreaks. A pre-deployment outbreak involved a WHO variant of interest (Theta) that had infected 4 international workers. Two additional predeployment clusters of infections were identified.

CONCLUSIONS

Our findings support that IH quarantine/testing protocols limited viral transmissions, halted offshore outbreaks, and stopped the spread of a variant of interest. The study demonstrates how genomic data can be used to understand viral transmission dynamics in employee populations and evaluate safety protocols in the offshore oil and gas industry.

Ultrafast Detection of SARS-CoV-2 Spike Protein (S) and Receptor-Binding Domain (RBD) in Saliva Using Surface-Enhanced Raman Spectroscopy

Controlling contagious diseases necessitates using diagnostic techniques that can detect infection in the early stages. Although different diagnostic tools exist, there are still challenges related to accuracy, rapidity, cost-effectiveness, and ease of use. Surface-enhanced Raman spectroscopy (SERS) is a rapid, simple, less expensive, and accurate method. We continue our previous work published on SERS detection of the SARS-CoV-2 receptor-binding domain (RBD) in water. In this work, we replace water with saliva to detect SARS-CoV-2 proteins at very low concentrations and during a very short time. We prepared a very low concentration of 10−9 M SARS-CoV-2 spike protein (S) and SARS-CoV-2 receptor-binding domain (RBD) in saliva to mimic a real case scenario. Then, we drop them on a SERS substrate. Using modified SERS measurements on the control and the sample containing the biomolecules, confirmed the sensitivity of the target identification. This technique provides different diagnostic solutions that are fast, simple, non-destructive and ultrasensitive. Simulation of the real-world of silicon wire covered with silver and gold, were performed using an effective and accurate tool, COMSOL Multiphysics software, for the enhancement properties study.

Outbreak investigation of airborne transmission of Omicron (B.1.1.529) - SARS-CoV-2 variant of concern in a restaurant: Implication for enhancement of indoor air dilution

Airborne transmission of SARS-CoV-2 has been increasingly recognized in the outbreak of COVID-19, especially with the Omicron variant. We investigated an outbreak due to Omicron variant in a restaurant. Besides epidemiological and phylogenetic analyses, the secondary attack rates of customers of restaurant-related COVID-19 outbreak before (Outbreak R1) and after enhancement of indoor air dilution (Outbreak R2) were compared. On 27th December 2021, an index case stayed in restaurant R2 for 98 min. Except for 1 sitting in the same table, six other secondary cases sat in 3 corners at 3 different zones, which were served by different staff. The median exposure time was 34 min (range: 19-98 min). All 7 secondary cases were phylogenetically related to the index. Smoke test demonstrated that the airflow direction may explain the distribution of secondary cases. Compared with an earlier COVID-19 outbreak in another restaurant R1 (19th February 2021), which occurred prior to the mandatory enhancement of indoor air dilution, the secondary attack rate among customers in R2 was significantly lower than that in R1 (3.4%, 7/207 vs 28.9%, 22/76, p<0.001). Enhancement of indoor air dilution through ventilation and installation of air purifier could minimize the risk of SARS-CoV-2 transmission in the restaurants.

Antigen Detection Tests for SARS-CoV-2: a systematic review and meta-analysis on real world data

Background and aim Rapid antigen detection (RAD) tests on nasopharyngeal specimens have been recently made available for SARS-CoV-2 infections, and early studies suggested their potential utilization as rapid screening and diagnostic testing. The present systematic review and meta-analysis was aimed to assess available evidence and to explore the reliability of antigenic tests in the management of the SARS-CoV-2 pandemic.

MATERIALS AND METHODS

We reported our meta-analysis according to the PRISMA statement. We searched Pubmed, Embase, and pre-print archive medRxiv.og for eligible studies published up to November 5th, 2020. Raw data included true/false positive and negative tests, and the total number of tests. Sensitivity and specificity data were calculated for every study, and then pooled in a random-effects model. Heterogeneity was assessed using the I2 measure. Reporting bias was assessed by means of funnel plots and regression analysis.

RESULTS

Based on 25 studies, we computed a pooled sensitivity of 72.8% (95%CI 62.4-81.3), a specificity of 99.4% (95%CI 99.0-99.7), with high heterogeneity and risk of reporting bias. More precisely, RAD tests exhibited higher sensitivity on samples with high viral load (i.e. <25 Cycle Threshold; 97.6%; 95%CI 94.1-99.0), compared to those with low viral load (≥25 Cycle Threshold; 43.6%; 95% 27.6-61.1).

DISCUSSION

As the majority of collected reports were either cohort or case-control studies, deprived of preventive power analysis and often oversampling positive tests, overall performances may have been overestimated. Therefore, the massive referral to antigenic tests in place of RT-qPCR is currently questionable, and also their deployment as mass screening test may lead to intolerable share of missing diagnoses. On the other hand, RAD tests may find a significant role in primary care and in front-line settings (e.g. Emergency Departments). (www.actabiomedica.it).

Heterogeneity and Risk of Bias in Studies Examining Risk Factors for Severe Illness and Death in COVID-19: A Systematic Review and Meta-Analysis

This systematic review and meta-analysis synthesized the evidence on the impacts of demographics and comorbidities on the clinical outcomes of COVID-19, as well as the sources of the heterogeneity and publication bias of the relevant studies. Two authors independently searched the literature from PubMed, Embase, Cochrane library, and CINAHL on 18 May 2021; removed duplicates; screened the titles, abstracts, and full texts by using criteria; and extracted data from the eligible articles. The variations among the studies were examined by using Cochrane, Q.; I2, and meta-regression. Out of 11,975 articles that were obtained from the databases and screened, 559 studies were abstracted, and then, where appropriate, were analyzed by meta-analysis (n = 542). COVID-19-related severe illness, admission to the ICU, and death were significantly correlated with comorbidities, male sex, and an age older than 60 or 65 years, although high heterogeneity was present in the pooled estimates. The study design, the study country, the sample size, and the year of publication contributed to this. There was publication bias among the studies that compared the odds of COVID-19-related deaths, severe illness, and admission to the ICU on the basis of the comorbidity status. While an older age and chronic diseases were shown to increase the risk of developing severe illness, admission to the ICU, and death among the COVID-19 patients in our analysis, a marked heterogeneity was present when linking the specific risks with the outcomes.

BNT162b2 vaccine induces antibody release in saliva: a possible role for mucosal viral protection?

Vaccination against an airborne pathogen is very effective if it induces also the development of mucosal antibodies that can protect against infection. The mRNA-based vaccine-encoding SARS-CoV-2 full-length spike protein (BNT162b2, Pfizer/BioNTech) protects also against infection despite being administered systemically. Here, we show that upon vaccination, cognate IgG molecules are also found in the saliva and are more abundant in SARS-CoV-2 previously exposed subjects, paralleling the development of plasma IgG. The antibodies titer declines at 3 months from vaccination. We identified a concentration of specific IgG in the plasma above which the relevant IgG can be detected in the saliva. Regarding IgA antibodies, we found only protease-susceptible IgA1 antibodies in plasma while they were present at very low levels in the saliva over the course of vaccination of SARS-CoV-2-naïve subjects. Thus, in response to BNT162b2 vaccine, plasma IgG can permeate into mucosal sites and participate in viral protection. It is not clear why IgA1 are detected in low amount, they may be proteolytically cleaved.

Evaluation of electropolymerized molecularly imprinted polymers (E-MIPs) on disposable electrodes for detection of SARS-CoV-2 in saliva

We investigate electropolymerized molecularly imprinted polymers (E-MIPs) for the selective recognition of SARS-CoV-2 whole virus. E-MIPs imprinted with SARS-CoV-2 pseudoparticles (pps) were electrochemically deposited onto screen printed electrodes by reductive electropolymerization, using the water-soluble N-hydroxmethylacrylamide (NHMA) as functional monomer and crosslinked with N,N'-methylenebisacrylamide (MBAm). E-MIPs for SARS-CoV-2 showed selectivity for template SARS-CoV-2 pps, with an imprinting factor of 3:1, and specificity (significance = 0.06) when cross-reacted with other respiratory viruses. E-MIPs detected the presence of SARS-CoV-2 pps in <10 min with a limit of detection of 4.9 log10 pfu/mL, suggesting their suitability for detection of SARS-CoV-2 with minimal sample preparation. Using electrochemical impedance spectroscopy (EIS) and principal component analysis (PCA), the capture of SARS-CoV-2 from real patient saliva samples was also evaluated. Fifteen confirmed COVID-19 positive and nine COVID-19 negative saliva samples were compared against the established loop-mediated isothermal nucleic acid amplification (LAMP) technique used by the UK National Health Service. EIS data demonstrated a PCA discrimination between positive and negative LAMP samples. A threshold real impedance signal (ZRe) ≫ 4000 Ω and a corresponding charge transfer resistance (RCT) ≫ 6000 Ω was indicative of absence of virus (COVID-19 negative) in agreement with values obtained for our control non-imprinted polymer control. A ZRe at or below a threshold value of 600 Ω with a corresponding RCT of <1200 Ω was indicative of a COVID-19 positive sample. The presence of virus was confirmed by treatment of E-MIPs with a SARS-CoV-2 specific monoclonal antibody.