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The genus Alphavirus harbors arboviruses of great concern, such as the Chikungunya virus and the equine encephalitis viruses. Transmission of pathogenic alphaviruses by mosquitoes could be influenced by insect-specific alphaviruses such as Eilat virus (EILV). However, insect-specific alphaviruses are rarely found in wild mosquitoes and only a few have been described in the literature. Here, we report the detection of EILV in a Culex univittatus mosquito from the north-eastern Namibian Zambezi region. Full genome analysis of MP458-NA-2018 showed 94.5% nucleotide identity to an EILV isolate from Israel. MP458-NA-2018 grouped with EILV in phylogenetic analysis and was placed within the clade of insect-specific alphaviruses. The virus was isolated in mosquito cells and shown to be restricted to insects as hosts by the inability to infect different vertebrate cell lines and a complete block of virus replication at 34°C. We further showed that infection of cells with EILV MP458-NA-2018 reduced production of infectious particles of Sindbis virus by 2000-fold over the entire course of infection, whereas reduction rates of Bagaza and Middleburg virus were approximately 3-10-fold and dependent on time after infection. While production of infectious particles of cells superinfected with the Chikungunya virus were approximately 30-fold reduced and more pronounced at a lower multiplicity of infection of 0.01, EILV seemed to enhance production of West Nile virus infectious particles by >5-fold when superinfected at a multiplicitiy of infection of 0.1. In summary, EILV from the Namibian Zambezi region influences in vitro replication of endemic flavi- and alphaviruses. [ABSTRACT FROM AUTHOR]

The genus Alphavirus harbors arboviruses of great concern, such as the Chikungunya virus and the equine encephalitis viruses. Transmission of pathogenic alphaviruses by mosquitoes could be influenced by insect-specific alphaviruses such as Eilat virus (EILV). However, insect-specific alphaviruses are rarely found in wild mosquitoes and only a few have been described in the literature. Here, we report the detection of EILV in a Culex univittatus mosquito from the north-eastern Namibian Zambezi region. Full genome analysis of MP458-NA-2018 showed 94.5% nucleotide identity to an EILV isolate from Israel. MP458-NA-2018 grouped with EILV in phylogenetic analysis and was placed within the clade of insect-specific alphaviruses. The virus was isolated in mosquito cells and shown to be restricted to insects as hosts by the inability to infect different vertebrate cell lines and a complete block of virus replication at 34°C. We further showed that infection of cells with EILV MP458-NA-2018 reduced production of infectious particles of Sindbis virus by 2000-fold over the entire course of infection, whereas reduction rates of Bagaza and Middleburg virus were approximately 3-10-fold and dependent on time after infection. While production of infectious particles of cells superinfected with the Chikungunya virus were approximately 30-fold reduced and more pronounced at a lower multiplicity of infection of 0.01, EILV seemed to enhance production of West Nile virus infectious particles by >5-fold when superinfected at a multiplicitiy of infection of 0.1. In summary, EILV from the Namibian Zambezi region influences in vitro replication of endemic flavi- and alphaviruses.

The entry and infectivity of a virus are determined by its interaction with the host. SARS-CoV-2, the virus responsible for COVID-19, utilizes the spike (S) protein to attach to and enter host cells. Recent studies have identified neuropilin-1 (NRP1) as a crucial facilitator for the entry of SARS-CoV-2. The binding of the spike protein to the b1 domain of NRP1 has been shown to enhance viral infection twofold. Consequently, targeting NRP1 to disrupt this interaction represents a promising strategy to mitigate viral infection. In this study, a small molecule library of approximately 10,000 compounds was screened to identify those that could inhibit the interaction between NRP1 and the spike protein by targeting the b1 domain of NRP1. The crystallographic structure of the b1 domain of human NRP1 (PDB entry: 7JJC) was used for this purpose. Following virtual screening, docking studies, and evaluation of binding affinity and ADMET properties, 10 compounds were shortlisted. The top two candidates, AZD3839 and LY2090314, were selected for molecular dynamics simulation studies over 100 ns to assess binding stability. MM/GBSA calculations indicated that both AZD3839 and LY2090314 exhibited strong and stable binding to the b1 domain of NRP1. Computational modeling of the interaction between the b1 domain of NRP1 and the receptor-binding domain of the spike protein suggested that AZD3839 and LY2090314 could effectively hinder the NRP1-spike interaction. Therefore, these compounds may serve as potential drug candidates to reduce SARS-CoV-2 infectivity. [ABSTRACT FROM AUTHOR]

At the beginning of the COVID-19 pandemic, diagnostic testing was not accessible for mildly ill or asymptomatic individuals. Military operational circumstances exclude the usage of reference laboratory tests. For that reason, at the beginning of the pandemic alternative test methods were needed in order to gain insight into the SARS-CoV-2 status of military personnel. The objectives of this study are to assess whether SARS-CoV-2 antibody rapid lateral flow assay (LFA) in combination with semi-autonomous SARS-CoV-2 antisense and sense genomic RNA fluorescence in situ hybridization (FISH) could establish disease status in military personnel in a fieldable setting, and to assess how this combination performed and to determine which type of sample performed best. A proof of concept sub-study regarding the SARS-CoV-2 application of the fieldable Biotrack-MED® FISH analyzer, a semi-autonomous multi-sample filter cytometer, preceded this observational prospective cohort pilot study. Dutch military personnel were included in the 26 June 2020–11 May 2021 period. Blood, nasopharyngeal and oropharyngeal swabs and saliva were tested at days 0 and 14. SPSS version 25 descriptive statistics and Cohen's kappa assessed agreement between test methods. Both the sensitivity and specificity of the field tests were calculated with ELISA and PCR as reference. Saliva appeared to be the preferred sample type for FISH, where blood was not useful. FISH analysis and LFA results had a concordance of 42% for testing negative, 30% for recovered from infection, 22% for ongoing—and 58% for acute infection in a reference laboratory lab result outcome (RT-PCR or ELISA respectively). The LFA results on serum and full blood corresponded with the ELISA-obtained results (kappa of 0.61 and 0.63 respectively at day 0 and 0.81 and 0.77 respectively at day 14). LFA (full blood-serum), FISH and RT-PCR on saliva did not reach the 90% sensitivity level advised by WHO, with 64–54, 38 and 71% at day 0 and 80–79, 53 and 24% at day 14 respectively. [ABSTRACT FROM AUTHOR]

Computational thinking (CT) is a set of problem-solving skills with high relevance in education and work contexts. The present paper explores the role of key cognitive factors underlying CT performance in non-programming university students. We collected data from 97 non-programming adults in higher education in a supervised setting. Fluid intelligence, crystallized intelligence, and visuospatial ability were assessed using computerized adaptive tests; CT was measured using the Computational Thinking test. The direct and indirect effects of gender and visuospatial ability through fluid intelligence on CT were tested in a serial multiple mediator model. Fluid intelligence predicted CT when controlling for the effects of gender, age, and visuospatial ability, while crystallized intelligence did not predict CT. Men had a small advantage in CT performance when holding the effects of cognitive abilities constant. Despite its large correlation with gender and CT, visuospatial ability did not directly influence CT performance. Overall, we found that programming-naive computational thinkers draw on their reasoning ability that does not rely on previously acquired knowledge to solve CT problems. Visuospatial ability and CT were spuriously associated. Drawing on the process overlap theory we propose that tests of fluid intelligence and CT sample an overlapping set of underlying visuospatial processes. [ABSTRACT FROM AUTHOR]

The effective reproduction number, Rt , is an important epidemiological metric used to assess the state of an epidemic, as well as the effectiveness of public health interventions undertaken in response. When Rt is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an Rt is below one indicates that new infections are decreasing, and so the epidemic is under control. There are several established software packages that are readily available to statistically estimate Rt using clinical surveillance data. However, there are comparatively few accessible tools for estimating Rt from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the R package ern that aims to perform the estimation of the effective reproduction number from real-world wastewater or aggregated clinical surveillance data in a user-friendly way. [ABSTRACT FROM AUTHOR]

Background: We previously demonstrated that when vaccines prevent infection, the dynamics of mixing between vaccinated and unvaccinated sub-populations is such that use of imperfect vaccines markedly decreases risk for vaccinated people, and for the population overall. Risks to vaccinated people accrue disproportionately from contact with unvaccinated people. In the context of the emergence of Omicron SARS-CoV-2 and evolving understanding of SARS-CoV-2 epidemiology, we updated our analysis to evaluate whether our earlier conclusions remained valid. Methods: We modified a previously published Susceptible-Infectious-Recovered (SIR) compartmental model of SARS-CoV-2 with two connected sub-populations: vaccinated and unvaccinated, with non-random mixing between groups. Our expanded model incorporates diminished vaccine efficacy for preventing infection with the emergence of Omicron SARS-CoV-2 variants, waning immunity, the impact of prior immune experience on infectivity, "hybrid" effects of infection in previously vaccinated individuals, and booster vaccination. We evaluated the dynamics of an epidemic within each subgroup and in the overall population over a 10-year time horizon. Results: Even with vaccine efficacy as low as 20%, and in the presence of waning immunity, the incidence of COVID-19 in the vaccinated subpopulation was lower than that among the unvaccinated population across the full 10-year time horizon. The cumulative risk of infection was 3–4 fold higher among unvaccinated people than among vaccinated people, and unvaccinated people contributed to infection risk among vaccinated individuals at twice the rate that would have been expected based on the frequency of contacts. These findings were robust across a range of assumptions around the rate of waning immunity, the impact of "hybrid immunity", frequency of boosting, and the impact of prior infection on infectivity in unvaccinated people. Interpretation: Although the emergence of the Omicron variants of SARS-CoV-2 has diminished the protective effects of vaccination against infection with SARS-CoV-2, updating our earlier model to incorporate loss of immunity, diminished vaccine efficacy and a longer time horizon, does not qualitatively change our earlier conclusions. Vaccination against SARS-CoV-2 continues to diminish the risk of infection among vaccinated people and in the population as a whole. By contrast, the risk of infection among vaccinated people accrues disproportionately from contact with unvaccinated people. [ABSTRACT FROM AUTHOR]

Diagnostic testing followed by isolation of identified cases with subsequent tracing and quarantine of close contacts—often referred to as test-trace-isolate-and-quarantine (TTIQ) strategy—is one of the cornerstone measures of infectious disease control. The COVID-19 pandemic has highlighted that an appropriate response to outbreaks of infectious diseases requires a firm understanding of the effectiveness of such containment strategies. To this end, mathematical models provide a promising tool. In this work, we present a delay differential equation model of TTIQ interventions for infectious disease control. Our model incorporates the assumption of limited TTIQ capacities, providing insights into the reduced effectiveness of testing and tracing in high prevalence scenarios. In addition, we account for potential transmission during the early phase of an infection, including presymptomatic transmission, which may be particularly adverse to a TTIQ based control. Our numerical experiments inspired by the early spread of COVID-19 in Germany demonstrate the effectiveness of TTIQ in a scenario where immunity within the population is low and pharmaceutical interventions are absent, which is representative of a typical situation during the (re-)emergence of infectious diseases for which therapeutic drugs or vaccines are not yet available. Stability and sensitivity analyses reveal both disease-dependent and disease-independent factors that impede or enhance the success of TTIQ. Studying the diminishing impact of TTIQ along simulations of an epidemic wave, we highlight consequences for intervention strategies. [ABSTRACT FROM AUTHOR]

Background: Halofuginone (PJS-539) is an oral prolyl-tRNA synthetase inhibitor that has a potent in vitro activity against SARS-CoV-2 virus. The safety and efficacy of halofuginone in Covid-19 patients has not been studied. Methods: We conducted a phase II, randomized, double-blind, placebo-controlled, dose ranging, safety and tolerability trial of halofuginone in symptomatic (≤ 7 days), mostly vaccinated, non-hospitalized adults with mild to moderate Covid-19. Patients were randomized in a 1:1:1 ratio to receive halofuginone 0.5mg, 1mg or placebo orally once daily for 10 days. The primary outcome was the decay rate of the SARS-CoV-2 viral load logarithmic curve within 10 days after randomization. Results: From September 25, 2021, to February 3, 2022, 153 patients were randomized. The mean decay rate in SARS-CoV-2 viral load log10 within 10 days was -3.75 (95% CI, -4.11; -3.19) in the placebo group, -3.83 (95% CI, -4.40; -2.27) in the halofuginone 0.5mg group and -4.13 (95% CI, -4.69; -3.57) in the halofuginone 1mg group, with no statistically significant difference in between placebo vs. halofuginone 0.5mg (mean difference -0.08; 95% CI -0.82 to 0.66, p = 0.96) and between placebo vs. halofuginone 1mg (mean difference -0.38; 95% CI, -1.11; 0.36, p = 0.41). There was no difference on bleeding episodes or serious adverse events at 28 days. Conclusions: Among non-hospitalized adults with mild to moderate Covid-19 halofuginone treatment was safe and well tolerated but did not decrease SARS-CoV-2 viral load decay rate within 10 days. [ABSTRACT FROM AUTHOR]

Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance. [ABSTRACT FROM AUTHOR]

Objectives: Since the declaration of the COVID-19 pandemic, many governments have imposed policies to reduce contacts between people who are presumed to be particularly vulnerable to dying from respiratory illnesses and the rest of the population. These policies typically address vulnerable individuals concentrated in centralized care facilities and entail limiting social contacts with visitors, staff members, and other care home residents. We use a standard epidemiological model to investigate the impact of such circumstances on the predicted infectious disease attack rates, for interacting robust and vulnerable populations. Methods: We implement a general susceptible-infectious-recovered (SIR) compartmental model with two populations: robust and vulnerable. The key model parameters are the per-individual frequencies of within-group (robust-robust and vulnerable-vulnerable) and between-group (robust-vulnerable and vulnerable-robust) infectious-susceptible contacts and the recovery times of individuals in the two groups, which can be significantly longer for vulnerable people. Results: Across a large range of possible model parameters including degrees of segregation versus intermingling of vulnerable and robust individuals, we find that concentrating the most vulnerable into centralized care facilities virtually always increases the infectious disease attack rate in the vulnerable group, without significant benefit to the robust group. Conclusions: Isolated care homes of vulnerable residents are predicted to be the worst possible mixing circumstances for reducing harm in epidemic or pandemic conditions. [ABSTRACT FROM AUTHOR]

The COVID-19 antibody test was developed to investigate the humoral immune response to SARS-CoV-2 infection. In this study, we examined whether S antibody titers measured using the anti-SARS-CoV-2 IgG II Quant assay (S-IgG), a high-throughput test method, reflects the neutralizing capacity acquired after SARS-CoV-2 infection or vaccination. To assess the antibody dynamics and neutralizing potency, we utilized a total of 457 serum samples from 253 individuals: 325 samples from 128 COVID-19 patients including 136 samples from 29 severe/critical cases (Group S), 155 samples from 71 mild/moderate cases (Group M), and 132 samples from 132 health care workers (HCWs) who have received 2 doses of the BNT162b2 vaccinations. The authentic virus neutralization assay, the surrogate virus neutralizing antibody test (sVNT), and the Anti-N SARS-CoV-2 IgG assay (N-IgG) have been performed along with the S-IgG. The S-IgG correlated well with the neutralizing activity detected by the authentic virus neutralization assay (0.8904. of Spearman's rho value, p < 0.0001) and sVNT (0.9206. of Spearman's rho value, p < 0.0001). However, 4 samples (2.3%) of S-IgG and 8 samples (4.5%) of sVNT were inconsistent with negative results for neutralizing activity of the authentic virus neutralization assay. The kinetics of the SARS-CoV-2 neutralizing antibodies and anti-S IgG in severe cases were faster than the mild cases. All the HCWs elicited anti-S IgG titer after the second vaccination. However, the HCWs with history of COVID-19 or positive N-IgG elicited higher anti-S IgG titers than those who did not have it previously. Furthermore, it is difficult to predict the risk of breakthrough infection from anti-S IgG or sVNT antibody titers in HCWs after the second vaccination. Our data shows that the use of anti-S IgG titers as direct quantitative markers of neutralizing capacity is limited. Thus, antibody tests should be carefully interpreted when used as serological markers for diagnosis, treatment, and prophylaxis of COVID-19. [ABSTRACT FROM AUTHOR]

Detection of subgenomic (sg) SARS-CoV-2 RNAs are frequently used as a correlate of viral infectiousness, but few data about correlation between sg load and viable virus are available. Here, we defined concordance between culture isolation and E and N sgRNA quantification by ddPCR assays in 51 nasopharyngeal swabs collected from SARS-CoV-2 positive hospitalized patients. Among the 51 samples, 14 were SARS-CoV-2 culture-positive and 37 were negative. According to culture results, the sensitivity and specificity of E and N sgRNA assays were 100% and 100%, and 84% and 86%, respectively. ROC analysis showed that the best E and N cut-offs to predict positive culture isolation were 32 and 161 copies/mL respectively, with an AUC (95% CI) of 0.96 (0.91–1.00) and 0.96 (0.92–1.00), and a diagnostic accuracy of 88% and 92%, respectively. Even if no significant correlations were observed between sgRNA amount and clinical presentation, a higher number of moderate/severe cases and lower number of days from symptoms onset characterized patients with sgRNA equal to or higher than sgRNA cut-offs. Overall, this study suggests that SARS-CoV-2 sgRNA quantification could be helpful to estimate the replicative activity of SARS-CoV-2 and can represent a valid surrogate marker to efficiently recognize patients with active infection. The inclusion of this assay in available SARS-CoV-2 diagnostics procedure might help in optimizing fragile patients monitoring and management. [ABSTRACT FROM AUTHOR]

Technology invention and implementation have resulted in long-term educational progress. This study aimed to identify the innovative strategies in determining the factors influencing in-service teachers' technology integration in China, focusing on the information and communication technology (ICT) integration. The sample consists of 685 in-service teachers. Four factors are found to influence in-service teachers' ICT integration: attitudes, self-efficacy, digital competence, and digital tools use. The results of the study utilizing the PLS-SEM approach demonstrated that all four factors have a substantial impact on in-service teachers' ICT integration and interact with each other. Meanwhile, attitudes, digital competence, and digital tools use have a mediating effect in this research. In addition, the study discussed the effects of gender, age, and teaching experience on influencing factors and ICT integration. This research provided beneficial insights for a successful design of instruction with ICT and contributed to innovative strategies for educational technology. [ABSTRACT FROM AUTHOR]

Patients with coronavirus 2019 (COVID-19) and obstructive sleep apnoea (OSA) have a worse prognosis than COVID-19 patients without OSA. This study aimed to examine the relationship between OSA risk and the severity of COVID-19 in patients undiagnosed with OSA. Patients diagnosed with COVID-19 and hospitalized or admitted to a community hotel were recruited for the study after recovery during a clinic check-up visit 6–8 weeks after discharge. At this visit, they answered the Epworth Sleeping Scale (ESS) and Berlin questionnaire. Demographic and clinical details were collected from electronic medical records. OSA risk was observed in 37 of 119 included patients (31.1%). Patients with high OSA risk were male, significantly older, had a higher body mass index (BMI), and had higher rates of hypertension and snoring than patients with low OSA risk. Moreover, OSA risk was associated with COVID-19 severity; 48.6% of patients with high risk for OSA suffered from severe COVID-19 compared to 22% of patients with low risk for OSA (p = 0.007). The duration of hospitalization for patients with a high OSA risk was 10.97±9.43 days, while that for those with a low OSA risk was 4.71±6.86 days (p = 0.001). After adjusting for BMI, age, hypertension, and chronic disease, the odds ratio was 4.3 (95%CI, 1.2–16, p = 0.029). A high OSA risk was associated with severe COVID-19 and longer hospitalization. Thus, we recommend that the Berlin and ESS questionnaires be completed for every COVID-19-infected patient at hospitalization, especially in the presence of comorbidities. [ABSTRACT FROM AUTHOR]

Objective: Validate the performance characteristics of two analyte specific, laboratory developed tests (LDTs) for the quantification of SARS-CoV-2 subgenomic RNA (sgRNA) and viral load on the Hologic Panther Fusion® using the Open Access functionality. Methods: Custom-designed primers/probe sets targeting the SARS-CoV-2 Envelope gene (E) and subgenomic E were optimized. A 20-day performance validation following laboratory developed test requirements was conducted to assess assay precision, accuracy, analytical sensitivity/specificity, lower limit of detection and reportable range. Results: Quantitative SARS-CoV-2 sgRNA (LDT-Quant sgRNA) assay, which measures intermediates of replication, and viral load (LDT-Quant VLCoV) assay demonstrated acceptable performance. Both assays were linear with an R2 and slope equal to 0.99 and 1.00, respectively. Assay precision was evaluated between 4–6 Log10 with a maximum CV of 2.6% and 2.5% for LDT-Quant sgRNA and LDT-Quant VLCoV respectively. Using negative or positive SARS-CoV-2 human nasopharyngeal swab samples, both assays were accurate (kappa coefficient of 1.00 and 0.92). Common respiratory flora and other viral pathogens were not detected and did not interfere with the detection or quantification by either assay. Based on 95% detection, the assay LLODs were 729 and 1206 Copies/mL for the sgRNA and VL load LDTs, respectively. Conclusion: The LDT-Quant sgRNA and LDT-Quant VLCoV demonstrated good analytical performance. These assays could be further investigated as alternative monitoring assays for viral replication; and thus, medical management in clinical settings which could inform isolation/quarantine requirements. [ABSTRACT FROM AUTHOR]

During the pandemic of COVID-19, numerous waves of infections affected the two hemispheres with different impacts on each country. Throughout these waves, and with the emergence of new variants, health systems and scientists have tried to provide real-time responses to the complex biology of SARS-CoV-2, dealing with different clinical presentations, biological characteristics, and clinical impact of these variants. In this context, knowing the extent period in which an infected individual releases infectious viral particles has important implications for public health. This work aimed to investigate viral RNA shedding and infectivity of SARS-CoV-2 beyond 10 days after symptom onset (SO). A prospective multicenter study was performed between July/2021 and February/2022 on 116 immunized strategic personnel with COVID-19 diagnosed by RT-qPCR, with asymptomatic (7%), mild (91%) or moderate disease (2%). At the time of diagnosis, 70% had 2 doses of vaccines, 26% had 2 plus a booster, and 4% had one dose. After day 10 from SO, sequential nasopharyngeal swabs were taken to perform RT-qPCR, viral isolation, and S gene sequencing when possible. Viral sequences were obtained in 98 samples: 43% were Delta, 16% Lambda, 15% Gamma, 25% Omicron (BA.1) and 1% Non-VOC/VOI, in accordance with the main circulating variants at each moment. SARS-CoV-2 RNA was detected 10 days post SO in 57% of the subjects. Omicron was significantly less persistent. Noteworthy, infective viruses could not be isolated in any of the samples. In conclusion, a 10-days isolation period was useful to prevent further infections, and proved valid for the variants studied. Recently, even shorter periods have been applied, as the Omicron variant is prevalent, and worldwide population is largely vaccinated. In the future, facing the possible emergence of new variants and considering immunological status, a return to 10 days may be necessary. [ABSTRACT FROM AUTHOR]

Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals. [ABSTRACT FROM AUTHOR]

Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring SARS-CoV-2 infection trends throughout the COVID-19 pandemic. Population biomarkers that measure the relative human fecal contribution to normalize SARS-CoV-2 wastewater concentrations are needed for improved analysis and interpretation of community infection trends. The Centers for Disease Control and Prevention National Wastewater Surveillance System (CDC NWSS) recommends using the wastewater flow rate or human fecal indicators as population normalization factors. However, there is no consensus on which normalization factor performs best. In this study, we provided the first multistate assessment of the effects of flow rate and human fecal indicators (crAssphage, F+ Coliphage, and PMMoV) on the correlation of SARS-CoV-2 wastewater concentrations and COVID-19 cases using the CDC NWSS dataset of 182 communities across six U.S. states. Flow normalized SARS-CoV-2 wastewater concentrations produced the strongest correlation with COVID-19 cases. The correlation from the three human fecal indicators were significantly lower than flow rate. Additionally, using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) significantly improved correlation values over samples that were analyzed with real-time reverse transcription quantitative polymerase chain reaction (rRT-qPCR). Our assessment shows that utilizing flow normalization with RT-ddPCR generate the strongest correlation between SARS-CoV-2 wastewater concentrations and COVID-19 cases. [ABSTRACT FROM AUTHOR]

Saliva has been a COVID-19 diagnostic specimen of interest due to its simple collection, scalability, and yield. Yet COVID-19 testing and estimates of the infectious period remain largely based on nasopharyngeal and nasal swabs. We sought to evaluate whether saliva testing captured prolonged presence of SARS-CoV-2 and potential infectiousness later in the disease course. We conducted an observational study of symptomatic COVID-19 patients at University Hospital in Newark, NJ. Paired saliva and nasal specimens from 96 patients were analyzed, including longitudinal analysis of paired observations from 28 of these patients who had multiple time-points. Saliva detected significantly more cases of COVID-19 beyond 5 days (86.1% [99/115] saliva vs 48.7% [56/115] nasal, p-value < 0.001), 9 days (79.4% [50/63] saliva vs 36.5% [23/63] nasal, p-value < 0.001) and 14 days (71.4% [20/28] saliva vs 32.1% [9/28] nasal, p-value = 0.010) of symptoms. Additionally, saliva yielded lower cycle thresholds across all time periods, indicative of higher viral loads in saliva. In the longitudinal analysis, a log-rank analysis indicated that the survival curve for saliva was significantly different from the curve for nasal swabs (p<0.001) with a median survival time for saliva of 18 days compared to 13 days for nasal swabs. We additionally performed saliva viral cultures among a similar COVID-19 patient cohort and noted patients with positive saliva viral cultures between 7 to 28 days of symptoms. Findings from this study suggest that SARS-CoV-2 RNA persists longer and in higher abundance in saliva compared to nasal swabs, with potential of prolonged propagating virus. Testing saliva may thus increase yield for detecting potentially infectious virus even beyond the first five days of symptomatic COVID-19. [ABSTRACT FROM AUTHOR]

Effective measures are needed to prevent the spread and infectivity of SARS-CoV-2 that causes COVID-19. Chemical inactivation may help to prevent the spread and transmission of this and other viruses. Hence, we tested the SARS-CoV-2 antiviral activity of acetic acid, the main component of vinegar, in vitro. Inactivation and binding assays suggest that acetic acid is virucidal. We found that 6% acetic acid, a concentration typically found in white distilled vinegar, effectively inactivated SARS-CoV-2 after 15-min incubation with a complete loss of replication of competent virus as measured by TCID50. Transmission electron microscopy further demonstrated that 6% acetic acid disrupts SARS-CoV-2 virion structure. In addition, 6% acetic acid significantly inhibits and disrupts the binding of SARS-CoV-2 spike protein binding to ACE2, the primary SARS-CoV-2 cell receptor, after contact with spike protein for 5, 10, 30 and 60 minutes incubation. Taken together, our findings demonstrate that acetic acid possesses inactivating activity against SARS-CoV-2 and may represent a safe alternative to commonly used chemical disinfectants to effectively control the spread of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

The screening of flu-like syndrome is difficult due to nonspecific symptoms or even oligosymptomatic presentation and became even more complex during the Covid-19 pandemic. However, an efficient screening tool plays an important role in the control of highly contagious diseases, allowing more efficient medical-epidemiological approaches and rational management of global health resources. Infrared thermography is a technique sensitive to small alterations in the skin temperature which may be related to early signs of inflammation and thus being relevant in the detection of infectious diseases. Thus, the objective of this study was to evaluate the potential of facial thermal profiles as a risk evaluator of symptoms and signs of SARs diseases, using COVID-19 as background disease. A total of 136 patients were inquired about the most common symptoms of COVID-19 infection and were submitted to an infrared image scanning, where the temperatures of 10 parameters from different regions of the face were captured. We used RT-qPCR as the ground truth to compare with the thermal parameters, in order to evaluate the performance of infrared imaging in COVID-19 screening. Only 16% of infected patients had fever at the hospital admission, and most infrared thermal variables presented values of temperature significantly higher in infected patients. The maximum eye temperature (MaxE) showed the highest predictive value at a cut-off of >35.9°C (sn = 71.87%, sp = 86.11%, LR+ = 5.18, LR- = 0.33, AUC = 0.850, p < 0.001). Our predictive model reached an accuracy of 86% for disease detection, indicating that facial infrared thermal scanning, based on the combination of different facial regions and the thermal profile of the face, has potential to act as a more accurate diagnostic support method for early COVID-19 screening, when compared to classical infrared methods, based on a single spot with the maximum skin temperature of the face. [ABSTRACT FROM AUTHOR]

Introduction: Non-pharmaceutical interventions (NPIs) such as lockdown, social distancing and use of face coverings was adopted by the United Kingdom (UK) Armed Forces (AF) during the COVID-19 pandemic. This study assessed the impact of the use of NPIs on the incidence of influenza-like illness (ILI) in the UK AF. Methods: A longitudinal study design was adopted, and secondary data was analysed retrospectively. Clinical Read codes for ILI was used to generate data for flu seasons before and during the COVID-19 pandemic (September 2017 to April 2021). Results: Before the COVID-19 pandemic, the rate of reporting ILI was ~ 4% across all flu seasons. The count of ILI was 2.9%, 2.2% and 3.1% during 2017–18, 2018–19 and 2019–20 flu seasons respectively. During the COVID-19 pandemic, both the rate of reporting ILI (0.6%) and the count of ILI (0.5%) were significantly smaller (p <.001). The rate of reporting ILI was positively correlated with the count of ILI (r (2) =.97, p =.014). Influenza vaccination rate increased by 1.3% during the COVID-19 pandemic. Vaccination rate was negatively correlated with the rate of reporting ILI (r (2) = -.52, p = 0.24) and the count of ILI (r (2) = -.61, p = 0.19). However, this correlation was not significant. The use of NPIs was negatively correlated with the rate of reporting ILI (r (2) = -.99, p = <.001) and the count of ILI (r (2) = -.95, p = 0.026). The overall multiple regression performed was statistically significant (R2 = 0.94, F (1, 2) = 33.628, p = 0.028). The rate of reporting ILI significantly predicted the count of ILI (β = 0.609, p = 0.028) while vaccination rate did not significantly predict the count of ILI (β = -0.136, p = 0.677). Conclusions: The incidence of ILI in the UK AF was significantly reduced during the COVID-19 pandemic. The use of NPIs and the rate of reporting ILI significantly reduced the count of ILI. Being vaccinated for influenza did not significantly reduce the count of ILI. [ABSTRACT FROM AUTHOR]

Introduction: Surgical tracheostomy (ST) and Percutaneous dilatational tracheostomy (PDT) are classified as high-risk aerosol-generating procedures and might lead to healthcare workers (HCW) infection. Albeit the COVID-19 strain slightly released since the vaccination era, preventing HCW from infection remains a major economical and medical concern. To date, there is no study monitoring particle emissions during ST and PDT in a clinical setting. The aim of this study was to monitor particle emissions during ST and PDT in a swine model. Methods: A randomized animal study on swine model with induced acute respiratory distress syndrome (ARDS) was conducted. A dedicated room with controlled airflow was used to standardize the measurements obtained using an airborne optical particle counter. 6 ST and 6 PDT were performed in 12 pigs. Airborne particles (diameter of 0.5 to 3 μm) were continuously measured; video and audio data were recorded. The emission of particles was considered as significant if the number of particles increased beyond the normal variations of baseline particle contamination determinations in the room. These significant emissions were interpreted in the light of video and audio recordings. Duration of procedures, number of expiratory pauses, technical errors and adverse events were also analyzed. Results: 10 procedures (5 ST and 5 PDT) were fully analyzable. There was no systematic aerosolization during procedures. However, in 1/5 ST and 4/5 PDT, minor leaks and some adverse events (cuff perforation in 1 ST and 1 PDT) occurred. Human factors were responsible for 1 aerosolization during 1 PDT procedure. ST duration was significantly shorter than PDT (8.6 ± 1.3 vs 15.6 ± 1.9 minutes) and required less expiratory pauses (1 vs 6.8 ± 1.2). Conclusions: COVID-19 adaptations allow preventing for major aerosol leaks for both ST and PDT, contributing to preserving healthcare workers during COVID-19 outbreak, but failed to achieve a perfectly airtight procedure. However, with COVID-19 adaptations, PDT required more expiratory pauses and more time than ST. Human factors and adverse events may lead to aerosolization and might be more frequent in PDT. [ABSTRACT FROM AUTHOR]

Background: Family clusters offer a good opportunity to study viral transmission in a stable setting. We aimed to analyze the specific role of children in transmission of SARS-CoV-2 within households. Methods: A prospective, longitudinal, observational study, including children with documented acute SARS-CoV-2 infection attending 22 summer-schools in Barcelona, Spain, was performed. Moreover, other patients and families coming from other school-like environments that voluntarily accessed the study were also studied. A longitudinal follow-up (5 weeks) of the family clusters was conducted to determine whether the children considered to be primary cases were able to transmit the virus to other family members. The household reproduction number (Re*) and the secondary attack rate (SAR) were calculated. Results: 1905 children from the summer schools were screened for SARS-CoV-2 infection and 22 (1.15%) tested positive. Moreover, 32 additional children accessed the study voluntarily. Of these, 37 children and their 26 households were studied completely. In half of the cases (13/26), the primary case was considered to be a child and secondary transmission to other members of the household was observed in 3/13, with a SAR of 14.2% and a Re* of 0.46. Conversely, the SAR of adult primary cases was 72.2% including the kids that gave rise to the contact tracing study, and 61.5% without them, and the estimated Re* was 2.6. In 4/13 of the paediatric primary cases (30.0%), nasopharyngeal PCR was persistently positive > 1 week after diagnosis, and 3/4 of these children infected another family member (p<0.01). Conclusions: Children may not be the main drivers of the infection in household transmission clusters in the study population. A prolonged positive PCR could be associated with higher transmissibility. [ABSTRACT FROM AUTHOR]

Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel. [ABSTRACT FROM AUTHOR]

The viral load of patients infected with SARS-CoV-2 varies on logarithmic scales and possibly with age. Controversial claims have been made in the literature regarding whether the viral load distribution actually depends on the age of the patients. Such a dependence would have implications for the COVID-19 spreading mechanism, the age-dependent immune system reaction, and thus for policymaking. We hereby develop a method to analyze viral-load distribution data as a function of the patients' age within a flexible, non-parametric, hierarchical, Bayesian, and causal model. The causal nature of the developed reconstruction additionally allows to test for bias in the data. This could be due to, e.g., bias in patient-testing and data collection or systematic errors in the measurement of the viral load. We perform these tests by calculating the Bayesian evidence for each implied possible causal direction. The possibility of testing for bias in data collection and identifying causal directions can be very useful in other contexts as well. For this reason we make our model freely available. When applied to publicly available age and SARS-CoV-2 viral load data, we find a statistically significant increase in the viral load with age, but only for one of the two analyzed datasets. If we consider this dataset, and based on the current understanding of viral load's impact on patients' infectivity, we expect a non-negligible difference in the infectivity of different age groups. This difference is nonetheless too small to justify considering any age group as noninfectious. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID-19) was first identified in respiratory samples and was found to commonly cause cough and pneumonia. However, non-respiratory symptoms including gastrointestinal disorders are also present and a big proportion of patients test positive for the virus in stools for a prolonged period. In this cross-sectional study, we investigated viral load trends in stools and nasopharyngeal swabs and their correlation with multiple demographic and clinical factors. The study included 211 laboratory-confirmed cases suffering from a mild form of the disease and completing their isolation period at a non-hospital center in the United Arab Emirates. Demographic and clinical information was collected by standardized questionnaire and from the medical records of the patient. Of the 211 participants, 25% tested negative in both sample types at the time of this study and 53% of the remaining patients had detectable viral RNA in their stools. A positive fecal viral test was associated with male gender, diarrhea as a symptom, and hospitalization during infection. A positive correlation was also observed between a delayed onset of symptoms and a positive stool test. Viral load in stools positively correlated with, being overweight, exercising, taking antibiotics in the last 3 months and blood type O. The viral load in nasopharyngeal swabs, on the other hand, was higher for blood type A, and rhesus positive (Rh factor). Regression analysis showed no correlation between the viral loads measured in stool and nasopharyngeal samples in any given patient. The results of this work highlight the factors associated with a higher viral count in each sample. It also shows the importance of stool sample analysis for the follow-up and diagnosis of recovering COVID-19 patients. [ABSTRACT FROM AUTHOR]

Quantitative measurement of SARS-CoV-2 neutralizing antibodies is highly expected to evaluate immune status, vaccine response, and antiviral therapy. The Elecsys® Anti-SARS-CoV-2 S (Elecsys® anti-S) was developed to measure anti-SARS-CoV-2 S proteins. We sought to investigate whether Elecsys® anti-S can be used to predict neutralizing activities in patients' serums using an authentic virus neutralization assay. One hundred forty-six serum samples were obtained from 59 patients with COVID-19 at multiple time points. Of the 59 patients, 44 cases were included in Group M (mild 23, moderate 21) and produced 84 samples (mild 35, moderate 49), while 15 cases were included in Group S (severe 11, critical 4) and produced 62 samples (severe 43, critical 19). The neutralization assay detected 73% positive cases, and Elecsys® anti-S and Elecsys® Anti-SARS-CoV-2 (Elecsys® anti-N) showed 72% and 66% positive cases, respectively. A linear correlation between the Elecsys® anti-S assay and the neutralization assay were highly correlated (r = 0.7253, r2 = 0.5261) than a linear correlation between the Elecsys® anti-N and neutralization assay (r = 0.5824, r2 = 0.3392). The levels of Elecsys® anti-S antibody and neutralizing activities were significantly higher in Group S than in Group M after 6 weeks from onset of symptoms (p < 0.05). Conversely, the levels of Elecsys® anti-N were comparable in both groups. Three immunosuppressed patients, including cancer patients, showed low levels of anti-S and anti-N antibodies and neutralizing activities throughout the measurement period, indicating the need for careful follow-up. Our data indicate that Elecsys® anti-S can predict the neutralization antibodies in COVID-19. [ABSTRACT FROM AUTHOR]

By the peak of COVID-19 restrictions on April 8, 2020, up to 1.5 billion students across 188 countries were affected by the suspension of physical attendance in schools. Schools were among the first services to reopen as vaccination campaigns advanced. With the emergence of new variants and infection waves, the question now is to find safe protocols for the continuation of school activities. We need to understand how reliable these protocols are under different levels of vaccination coverage, as many countries have a meager fraction of their population vaccinated, including Uganda where the coverage is about 8%. We investigate the impact of face-to-face classes under different protocols and quantify the surplus number of infected individuals in a city. Using the infection transmission when schools were closed as a baseline, we assess the impact of physical school attendance in classrooms with poor air circulation. We find that (i) resuming school activities with people only wearing low-quality masks leads to a near fivefold city-wide increase in the number of cases even if all staff is vaccinated, (ii) resuming activities with students wearing good-quality masks and staff wearing N95s leads to about a threefold increase, (iii) combining high-quality masks and active monitoring, activities may be carried out safely even with low vaccination coverage. These results highlight the effectiveness of good mask-wearing. Compared to ICU costs, high-quality masks are inexpensive and can help curb the spreading. Classes can be carried out safely, provided the correct set of measures are implemented. Author summary: The World Bank-UNESCO-UNICEF report [1] estimates that learning losses from the COVID-19 pandemic could cost this generation $17 trillion dollars in lifetime earnings. Despite the surging pressure to keep schools open, many countries lack guidelines for safe school activities. Using the empirical transmission level for closed schools as a baseline, we quantify the impact of distinct non-pharmaceutical interventions (NPIs) on infection rates and different values of vaccine coverage. Strikingly, we show that classes can be kept safe, provided the correct wearing of good quality masks together with to the proper combination of other NPIs. In such scenarios, the increase in infections can be kept below 20% compared to suspending classes. [ABSTRACT FROM AUTHOR]

Purpose: To demonstrate the diagnostic performance of rapid SARS-CoV-2 RT-LAMP assays, comparing the performance of genomic versus sub-genomic sequence target with subsequent application in an asymptomatic screening population. Methods: RT-LAMP diagnostic specificity (DSe) and sensitivity (DSe) was determined using 114 RT-PCR clinically positive and 88 RT-PCR clinically negative swab samples processed through the diagnostic RT-PCR service within the University Hospitals of Leicester NHS Trust. A swab-based RT-LAMP SARS-CoV-2 screening programme was subsequently made available to all staff and students at the University of Leicester (Autumn 2020), implemented to ISO 15189:2012 standards using NHS IT infrastructure and supported by University Hospital Leicester via confirmatory NHS diagnostic laboratory testing of RT-LAMP 'positive' samples. Results: Validation samples reporting a Ct < 20 were detected at 100% DSe and DSp, reducing to 95% DSe (100% DSp) for all samples reporting a Ct < 30 (both genomic dual sub-genomic assays). Advisory screening identified nine positive cases in 1680 symptom free individuals (equivalent to 540 cases per 100,000) with results reported back to participants and feed into national statistics within 48 hours. Conclusion: This work demonstrates the utility of a rapid RT-LAMP assay for collapsing transmission of SARS-CoV-2 in an asymptomatic screening population. [ABSTRACT FROM AUTHOR]

Background: An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing. We evaluated clinical performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC rapid PCR test. Methods: We conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites where we collected two bilateral anterior nasal swabs and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the "gold standard". Results: We enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently SARS-CoV-2 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R = 0.89 [95% CI 0.81, 0.94]). Conclusions: DASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results (approximately 15 minutes) in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. [ABSTRACT FROM AUTHOR]

We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies—a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. Applying the model to those events yields results that suggest the following: (1) transmission was airborne; (2) superspreading events do not require an index patient with an unusually high viral load; (3) the viral loads for all of the index patients were of the same order of magnitude and consistent with experimentally measured values for patients at the onset of symptoms, even though viral loads across the population vary by a factor of >108. In particular we used a Wells-Riley exposure model to calculate q, the total average number of infectious quanta inhaled by a person at the event. Given the q value for each event, the simple airborne transmission model was used to determined Sq, the rate at which the index patient exhaled infectious quanta and N0, the characteristic number of COVID-19 virions needed to induce infection. Despite the uncertainties in the values of some parameters of the superspreading events, all five events yielded (N0∼300–2,000 virions), which is similar to published values for influenza. Finally, this work describes the conditions under which similar methods can provide actionable information on the transmission of other viruses. [ABSTRACT FROM AUTHOR]

Background: During the coronavirus-19 disease (COVID-19) pandemic, gastroenterology guidelines recommended the suspension or reduction of non-urgent endoscopy. We aimed to assess the appropriateness and safety of endoscopic activity during the pandemic first wave lockdown using European Society of Gastrointestinal Endoscopy (ESGE) recommendations. Methods: We identified scheduled patients from the onset of the lockdown in Spain since March 16, 2020) to April 14, 2020. Daily hospital COVID-19-related burden was also registered. A similar cohort from a period immediately before the lockdown was studied (pre-lockdown cohort) to compare appropriateness. Results: 454 endoscopy procedures were performed during the studied period, comprising a 49.7% reduction compared to the pre-lockdown cohort (n = 913). There was a significant increase in ESGE high-priority indications (62.1% vs. 45.6%, p<0.001) associated with an increase in relevant endoscopic findings (p = 0.006), advanced neoplasia/cancer (p = 0.004) and cancer detection rate (p = 0.010). There were no differences in the rate of admissions or infection among scheduled patients in the lockdown cohort. None of the staff members tested positive for COVID-19 in the 7 days after the adoption of protective measures. Conclusion: A prioritized endoscopic activity is not associated with higher contagion after adopting protective measures. In addition, a triage of procedures that follow the ESGE criteria increases the rate of relevant endoscopic findings. These considerations may reduce the impact of the delays of diagnosis after the pandemic. [ABSTRACT FROM AUTHOR]

Understanding antibody responses after natural severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can guide the coronavirus disease 2019 (COVID-19) vaccine schedule, especially in resource-limited settings. This study aimed to assess the dynamics of SARS-CoV-2 antibodies, including anti-spike protein 1 (S1) immunoglobulin (Ig)G, anti-receptor-binding domain (RBD) total Ig, anti-S1 IgA, and neutralizing antibody against wild-type SARS-CoV-2 over time in a cohort of patients who were previously infected with the wild-type SARS-CoV-2. Between March and May 2020, 531 individuals with virologically confirmed cases of wild-type SARS-CoV-2 infection were enrolled in our immunological study. Blood samples were collected at 3-, 6-, 9-, and 12-months post symptom onset or detection of SARS-CoV-2 by RT-PCR (in asymptomatic individuals). The neutralizing titers against SARS-CoV-2 were detected in 95.2%, 86.7%, 85.0%, and 85.4% of recovered COVID-19 patients at 3, 6, 9, and 12 months after symptom onset, respectively. The seropositivity rate of anti-S1 IgG, anti-RBD total Ig, anti-S1 IgA, and neutralizing titers remained at 68.6%, 89.6%, 77.1%, and 85.4%, respectively, at 12 months after symptom onset. We observed a high level of correlation between neutralizing and SARS-CoV-2 spike protein-specific antibody titers. The half-life of neutralizing titers was estimated at 100.7 days (95% confidence interval = 44.5–327.4 days, R2 = 0.106). These results support that the decline in serum antibody levels over time in both participants with severe disease and mild disease were depended on the symptom severity, and the individuals with high IgG antibody titers experienced a significantly longer persistence of SARS-CoV-2-specific antibody responses than those with lower titers. [ABSTRACT FROM AUTHOR]

Introduction: The novel coronavirus disease 2019 (COVID-19) has emerged as a global pandemic, and the United States and European authorities established criteria for the release of COVID-19 patients from isolation in October 2020. However, a huge discrepancy exists between the hospital-discharge protocol for COVID-19 patients and the release of patients from in-hospital isolation. Our initially proposed criteria for in-hospital release from isolation was not adhered to by healthcare workers (HCWs) due to prevailing concerns regarding disease infectivity. Herein, we report difficulties encountered in attempting to establish a common understanding of the management of emerging infections. Methods: We performed a Google Form-based questionnaire survey targeting HCWs from Okayama University Hospital, Japan, via e-mail on January 21–28, 2021. The anonymous investigation required respondents to provide information regarding their background as well as perceptions regarding the requirement, level of understanding, and readiness for developing release criteria. Results: We obtained 150 eligible responses, including 57 (38.0%) from medical doctors and 53 (35.3%) from nurses. Most HCWs managing COVID-19 patients advocated for the implementation of the criteria, whereas those not working in that capacity did not (p<0.001). Over half of the HCWs indicated discomfort at seeing COVID-19 patients transitioning to general management even after meeting the criteria. Conclusions: It was challenging to establish a common understanding regarding the ideal criteria for in-hospital release of COVID-19 patients from isolation in our hospital. The dissemination of our experiences and multifaceted discussions with HCWs would be of great value as a countermeasure against the emergent pandemic. [ABSTRACT FROM AUTHOR]

The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69–91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, the cause of COVID-19, requires reliable diagnostic methods to track the circulation of this virus. Following the development of RT-qPCR methods to meet this diagnostic need in January 2020, it became clear from interlaboratory studies that the reported Ct values obtained for the different laboratories showed high variability. Despite this the Ct values were explored as a quantitative cut off to aid clinical decisions based on viral load. Consequently, there was a need to introduce standards to support estimation of SARS-CoV-2 viral load in diagnostic specimens. In a collaborative study, INSTAND established two reference materials (RMs) containing heat-inactivated SARS-CoV-2 with SARS-CoV-2 RNA loads of ~107 copies/mL (RM 1) and ~106 copies/mL (RM 2), respectively. Quantification was performed by RT-qPCR using synthetic SARS-CoV-2 RNA standards and digital PCR. Between November 2020 and February 2021, German laboratories were invited to use the two RMs to anchor their Ct values measured in routine diagnostic specimens, with the Ct values of the two RMs. A total of 305 laboratories in Germany were supplied with RM 1 and RM 2. The laboratories were requested to report their measured Ct values together with details on the PCR method they used to INSTAND. This resultant 1,109 data sets were differentiated by test system and targeted gene region. Our findings demonstrate that an indispensable prerequisite for linking Ct values to SARS-CoV-2 viral loads is that they are treated as being unique to an individual laboratory. For this reason, clinical guidance based on viral loads should not cite Ct values. The RMs described were a suitable tool to determine the specific laboratory Ct for a given viral load. Furthermore, as Ct values can also vary between runs when using the same instrument, such RMs could be used as run controls to ensure reproducibility of the quantitative measurements. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has drastically shifted the way people work. While many businesses can operate remotely, a large number of jobs can only be performed on-site. Moreover as businesses create plans for bringing workers back on-site, they are in need of tools to assess the risk of COVID-19 for their employees in the workplaces. This study aims to fill the gap in risk modeling of COVID-19 outbreaks in facilities like offices and warehouses. We propose a simulation-based stochastic contact network model to assess the cumulative incidence in workplaces. First-generation cases are introduced as a Bernoulli random variable using the local daily new case rate as the success rate. Contact networks are established through randomly sampled daily contacts for each of the first-generation cases and successful transmissions are established based on a randomized secondary attack rate (SAR). Modification factors are provided for SAR based on changes in airflow, speaking volume, and speaking activity within a facility. Control measures such as mask wearing are incorporated through modifications in SAR. We validated the model by comparing the distribution of cumulative incidence in model simulations against real-world outbreaks in workplaces and nursing homes. The comparisons support the model's validity for estimating cumulative incidences for short forecasting periods of up to 15 days. We believe that the current study presents an effective tool for providing short-term forecasts of COVID-19 cases for workplaces and for quantifying the effectiveness of various control measures. The open source model code is made available at github.com/abhineetgupta/covid-workplace-risk. [ABSTRACT FROM AUTHOR]

Reverse transcription–quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time–reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic. [ABSTRACT FROM AUTHOR]

Introduction: Coronavirus disease 2019 (COVID-19) has led to radical changes in social distancing awareness and affected social relationships. Owing to large-scale lockdown, home quarantine and social distancing requirements, it was anticipated that sexual activities would be severely impacted. However, retrospective self-report studies showed that pornography use and autoerotism increased during the pandemic. Aim: This study used big-data databases available on the Internet to investigate factors that modulated pornography use during the pandemic. Methods: Daily relative search volume (RSV) data from Google Trends for the period from 24 February 2020 to 13 July 2020 were extracted. Pornhub traffic data were extracted from the Pornhub Insights website, for the period from 24 February 2020 to 13 July 2020. The parameter was defined as 'percent change in traffic compared to an average day in 2019'. The number of daily new cases of COVID-19 was extracted from the database on Our World in Data. Outcome measures: The normality of the data was examined using the Shapiro-Wilk test. All variables included in this study were non-normally distributed. Therefore, non-parametric tests or parametric tests with bootstrapping were adopted where appropriate. Results: According to Google Trends, the RSV for 'pornography' increased after late March 2020, which is close to the date when the World Health Organization declared COVID-19 a global pandemic. The number of daily new cases of COVID-19 was positively correlated with the traffic of Pornhub, a popular pornography website, and the RSV for 'pornography'. Moderation analysis demonstrated a significant main effect of daily new cases of COVID-19 and the RSV for 'social distancing' in predicting Pornhub traffic/RSV for 'pornography'. Furthermore, the RSV for 'social distancing' significantly moderated the relationship between daily new cases and Pornhub traffic/RSV for 'pornography'. A stronger COVID-pornography use association was observed with increased social distancing awareness. Conclusion: Increased pornography consumption during the pandemic was observed, and it was associated with the severity of the pandemic. Social distancing awareness could be a key factor influencing interest in and use of pornography. Further studies on the changes in sexual desire and birth-rate control are worthwhile because long-term public health may be affected by the changes in sexual behaviour during the pandemic. [ABSTRACT FROM AUTHOR]

Objectives: To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/μL. Methods: A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset. The model was then used to convert the stored cycle threshold values of a large dataset of 6208 diagnostic samples into copies/μL of SARS-CoV-2. The calculated viral load was used for a single cohort retrospective study. Finally, the cohort was randomly divided into a training set (n = 3095) and an evaluation set (n = 3113) to establish a logistic regression model for predicting case-fatality and to assess its accuracy. Results: The model for converting the Ct values into copies/μL was suitably accurate. The calculated viral load over time in the cohort of Covid-19 positive samples showed very low viral loads during the summer inter-epidemic waves in Italy. The calculated viral load along with gender and age allowed building a predictive model of case-fatality probability which showed high specificity (99.0%) and low sensitivity (21.7%) at the optimal threshold which varied by modifying the threshold (i.e. 75% sensitivity and 83.7% specificity). Alternative models including categorised cVL or raw cycle thresholds obtained by the same diagnostic method also gave the same performance. Conclusion: The modelling of the cycle threshold values using digital PCR had the potential of fostering studies addressing issues regarding Sars-CoV-2; furthermore, it may allow setting up predictive tools capable of early identifying those patients at high risk of case-fatality already at diagnosis, irrespective of the diagnostic RT-qPCR platform in use. Depending upon the epidemiological situation, public health authority policies/aims, the resources available and the thresholds used, adequate sensitivity could be achieved with acceptable low specificity. [ABSTRACT FROM AUTHOR]

The rapid development of advanced technology worldwide has promoted an increase in the need for highly skilled engineers who are adept at applying job-related technologies and have engineering competency (ENcom) to gain knowledge and introduce creative solutions. However, little is known about the underlying mechanism of the associations between ICT competencies related to work (ICT-Work) and the ENcom of engineering students. This study sought to examine the role of ICT-Work on ENcom. Based on the literature, self-esteem and self-regulated learning (SRL) were identified as factors that indicate the effect of ICT-Work on ENcom, while gender was identified as a moderator that conditioned these mediated relationships. The sample consisted of 1,313 undergraduate engineering students from eleven universities in Thailand. The results of structural equation modeling (SEM) showed positive direct and indirect effects of ICT-Work on ENcom, self-esteem, and SRL and confirmed that self-esteem and SRL mediate the impact of ICT-Work on ENcom. Moreover, multigroup SEM revealed no gender differences in the factor loadings and structural path coefficients of ICT-Work on ENcom via self-esteem and SRL. To prepare students for their professional lives in the digital world, educational institutions should emphasize the importance of developing engineering students in ICT-Work and the use of advanced ICT involved in the job. [ABSTRACT FROM AUTHOR]

Aims: Patients with cardiovascular comorbidities have a significantly increased risk for a critical course of COVID-19. As the SARS-CoV2 virus enters cells via the angiotensin-converting enzyme receptor II (ACE2), drugs which interact with the renin angiotensin aldosterone system (RAAS) were suspected to influence disease severity. Methods and results: We analyzed 1946 consecutive patients with cardiovascular comorbidities or hypertension enrolled in one of the largest European COVID-19 registries, the Lean European Open Survey on SARS-CoV-2 (LEOSS) registry. Here, we show that angiotensin II receptor blocker intake is associated with decreased mortality in patients with COVID-19 [OR 0.75 (95% CI 0,59–0.96; p = 0.013)]. This effect was mainly driven by patients, who presented in an early phase of COVID-19 at baseline [OR 0,64 (95% CI 0,43–0,96; p = 0.029)]. Kaplan-Meier analysis revealed a significantly lower incidence of death in patients on an angiotensin receptor blocker (ARB) (n = 33/318;10,4%) compared to patients using an angiotensin-converting enzyme inhibitor (ACEi) (n = 60/348;17,2%) or patients who received neither an ACE-inhibitor nor an ARB at baseline in the uncomplicated phase (n = 90/466; 19,3%; p<0.034). Patients taking an ARB were significantly less frequently reaching the mortality predicting threshold for leukocytes (p<0.001), neutrophils (p = 0.002) and the inflammatory markers CRP (p = 0.021), procalcitonin (p = 0.001) and IL-6 (p = 0.049). ACE2 expression levels in human lung samples were not altered in patients taking RAAS modulators. Conclusion: These data suggest a beneficial effect of ARBs on disease severity in patients with cardiovascular comorbidities and COVID-19, which is linked to dampened systemic inflammatory activity. [ABSTRACT FROM AUTHOR]

Introduction: We aimed to examine if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) cycle quantification (Cq) value, as a surrogate for SARS-CoV-2 viral load, could predict hospitalisation and disease severity in adult patients with coronavirus disease 2019 (COVID-19). Methods: We performed a prospective cohort study of adult patients with PCR positive SARS-CoV-2 airway samples including all out-patients registered at the Department of Infectious Diseases, Odense University Hospital (OUH) March 9-March 17 2020, and all hospitalised patients at OUH March 10-April 21 2020. To identify associations between Cq-values and a) hospital admission and b) a severe outcome, logistic regression analyses were used to compute odds ratios (OR) and 95% Confidence Intervals (CI), adjusting for confounding factors (aOR). Results: We included 87 non-hospitalised and 82 hospitalised patients. The median baseline Cq-value was 25.5 (interquartile range 22.3–29.0). We found a significant association between increasing Cq-value and hospital-admission in univariate analysis (OR 1.11, 95% CI 1.04–1.19). However, this was due to an association between time from symptom onset to testing and Cq-values, and no association was found in the adjusted analysis (aOR 1.08, 95% CI 0.94–1.23). In hospitalised patients, a significant association between lower Cq-values and higher risk of severe disease was found (aOR 0.89, 95% CI 0.81–0.98), independent of timing of testing. Conclusions: SARS-CoV-2 PCR Cq-values in outpatients correlated with time after symptom onset, but was not a predictor of hospitalisation. However, in hospitalised patients lower Cq-values were associated with higher risk of severe disease. [ABSTRACT FROM AUTHOR]

Introduction: Mildly symptomatic cases of Covid-19 in previously-well individuals form the majority of infections and also serve as potent vectors of transmission. The factors affecting the duration of SARS-CoV-2 RNA viral shedding (DVS) in these patients remain largely unknown. Objectives: To perform a systematic analysis of the clinical, radiologic, laboratory investigations in patients with few comorbidities infected with mild Covid-19 to identify factors associated with the DVS. Methods: In this retrospective cohort study, patients with mild or asymptomatic Covid-19 were included. Baseline characteristics including age, nationality, comorbidities, concomitant medications, and type of isolation arrangement in the facility (single or in pairs) were collected. Clinical features and radiologic/haematologic findings were also collected. Taking day 28 as the cut-off, 187 patients who had a negative swab result up to day 28 (no prolonged DVS) were compared to 126 patients with a persistently positive result on or after day 28 (prolonged DVS). Results: Of 964 consecutive patients included, 851 (88.3%) patients were symptomatic. 266 patients had a documented negative RT-PCR assay with a median DVS of 25 days (range: 13 to 96 days; interquartile range (IQR): 22 to 33 days). Patients isolated in pairs were associated with prolonged DVS (OR: 2.7; 95% CI: 1.7 to 4.5; p<0.0001) compared to those isolated individually. Among vital signs, only tachycardia was associated with prolonged DVS (OR: 2.6; 95% CI: 1.0 to 7.1; p = 0.03). Amongst investigations, only a raised CRP was associated with prolonged DVS (OR: 2.7; 95% CI: 1.1 to 6.8; p = 0.02). Conclusions: In young, mildly symptomatic Covid-19 patients, prolonged DVS was associated with being isolated in pairs compared to individually. In situations where a negative RT-PCR test result is required, retesting in patients who were not isolated individually, or who had baseline tachycardia or a raised CRP, may be delayed to increase the yield of a negative result. [ABSTRACT FROM AUTHOR]

Background & aim: We investigated the combination of rapid antigen detection (RAD) and RT-qPCR assays in a stepwise procedure to optimize the detection of COVID-19. Methods: From August 2020 to November 2020, 43,399 patients were screened in our laboratory for COVID-19 diagnostic by RT-qPCR using nasopharyngeal swab. Overall, 4,691 of the 43,399 were found to be positive, and 200 were retrieved for RAD testing allowing comparison of diagnostic accuracy between RAD and RT-qPCR. Cycle threshold (Ct) and time from symptoms onset (TSO) were included as covariates. Results: The overall sensitivity, specificity, PPV, NPV, LR-, and LR+ of RAD compared with RT-qPCR were 72% (95%CI 62%–81%), 99% (95% CI95%–100%), 99% (95%CI 93%–100%), and 78% (95%CI 70%–85%), 0.28 (95%CI 0.21–0.39), and 72 (95%CI 10–208) respectively. Sensitivity was higher for patients with Ct ≤ 25 regardless of TSO: TSO ≤ 4 days 92% (95%CI 75%–99%), TSO > 4 days 100% (95%CI 54%–100%), and asymptomatic 100% (95%CI 78–100%). Overall, combining RAD and RT-qPCR would allow reducing from only 4% the number of RT-qPCR needed. Conclusions: This study highlights the risk of misdiagnosing COVID-19 in 28% of patients if RAD is used alone. A stepwise analysis that combines RAD and RT-qPCR would be an efficient screening procedure for COVID-19 detection and may facilitate the control of the outbreak. [ABSTRACT FROM AUTHOR]

Background: Prolonged periods of confined living on a cruise ship increase the risk for respiratory disease transmission. We describe the epidemiology and clinical characteristics of a SARS-CoV-2 outbreak in Australian passengers on the Diamond Princess cruise ship and provide recommendations to mitigate future cruise ship outbreaks. Methods: We conducted a retrospective cohort study of Australian passengers who travelled on the Diamond Princess from 20 January until 4 February 2020 and were either hospitalised, remained in Japan or repatriated. The main outcome measures included an epidemic curve, demographics, symptoms, clinical and radiological signs, risk factors and length of time to clear infection. Results: Among 223 Australian passengers, 56 were confirmed SARS-CoV-2 positive. Forty-nine cases had data available and of these over 70% had symptoms consistent with COVID-19. Of symptomatic cases, 17% showed signs and symptoms before the ship implemented quarantine and a further two-thirds had symptoms within one incubation period of quarantine commencing. Prior to ship-based quarantine, exposure to a close contact or cabin mate later confirmed SARS-CoV-2 positive was associated with a 3.78 fold (95% CI, 2.24–6.37) higher risk of COVID-19 acquisition compared to non-exposed passengers. Exposure to a positive cabin mate during the ship's quarantine carried a relative risk of 6.18 (95% CI, 1.96–19.46) of developing COVID-19. Persistently asymptomatic cases represented 29% of total cases. The median time to the first of two consecutive negative PCR-based SARS-CoV-2 assays was 13 days for asymptomatic cases and 19 days for symptomatic cases (p = 0.002). Conclusion: Ship based quarantine was effective at reducing transmission of SARS-CoV-2 amongst Australian passengers, but the risk of infection was higher if an individual shared a cabin or was a close contact of a confirmed case. Managing COVID-19 in cruise ship passengers is challenging and requires enhanced health measures and access to onshore quarantine and isolation facilities. [ABSTRACT FROM AUTHOR]

The widespread use of facemasks throughout the population is recommended by the WHO to reduce transmission of the SARS-CoV-2 virus. As some regions of the world are facing mask shortages, reuse may be necessary. However, used masks are considered as a potential hazard that may spread and transmit disease if they are not decontaminated correctly and systematically before reuse. As a result, the inappropriate decontamination practices that are commonly witnessed in the general public are challenging management of the epidemic at a large scale. To achieve public acceptance and implementation, decontamination procedures need to be low-cost and simple. We propose the use of hot hygroscopic materials to decontaminate non-medical facemasks in household settings. We report on the inactivation of a viral load on a facial mask exposed to hot hygroscopic materials for 15 minutes. As opposed to recent academic studies whereby decontamination is achieved by maintaining heat and humidity above a given value, a more flexible procedure is proposed here using a slow decaying pattern, which is both effective and easier to implement, suggesting straightforward public deployment and hence reliable implementation by the population. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic is far more than a health crisis: it has unpredictably changed our whole way of life. As suggested by the analysis of economic data on sales, this dramatic scenario has also heavily impacted individuals' spending levels. To better understand these changes, the present study focused on consumer behavior and its psychological antecedents. Previous studies found that crises differently affect people's willingness to buy necessities products (i.e., utilitarian shopping) and non-necessities products (i.e., hedonic shopping). Therefore, in examining whether changes in spending levels were associated with changes in consumer behavior, we adopted a fine-grained approach disentangling between necessities and non-necessities. We administered an online survey to 3833 participants (age range 18–64) during the first peak period of the contagion in Italy. Consumer behavior toward necessities was predicted by anxiety and COVID-related fear, whereas consumer behavior toward non-necessities was predicted by depression. Furthermore, consumer behavior toward necessities and non-necessities was predicted by personality traits, perceived economic stability, and self-justifications for purchasing. The present study extended our understanding of consumer behavior changes during the COVID-19 pandemic. Results could be helpful to develop marketing strategies that consider psychological factors to meet actual consumers' needs and feelings. [ABSTRACT FROM AUTHOR]