Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Validation of the United States isolation termination criteria using virus culture results of the omicron variant in Japan

Cycle threshold (Ct) values obtained from real-time reverse-transcription polymerase chain reaction (RT-PCR) tests are commonly used to determine COVID-19 isolation discharge from hospitals. However, not all patients with low Ct values are infectious, and studies evaluating infectivity through virus cultures in Japan remain limited. This study assessed patients with Ct values <30 at 10 days after symptom onset and compared the clinical characteristics of seven patients with positive virus culture results and 11 patients with negative virus culture results to validate the Centers for Disease Control and Prevention (CDC) isolation criteria in Japan. Among non-immunosuppressed patients with mild-to-moderate COVID-19, 80 % were virus culture-negative 10 days after symptom onset, even when the Ct values were <30. In contrast, only 33 % of patients with severe-to-critical symptoms tested negative on virus culture. All immunosuppressed patients with severe-to-critical symptoms consistently tested positive in virus cultures. Notably, three patients with hematological disorders remained virus culture-positive 20 days after symptom onset. These findings generally align with the CDC criteria. For non-immunosuppressed patients with mild-to-moderate COVID-19, isolation release after 10 days is supported without the need for additional RT-PCR testing. However, for non-immunosuppressed patients with severe-to-critical symptoms and immunocompromised patients, particularly those with hematological disorders, isolation may be safely discontinued when Ct values exceed 30 after 10 days. This study provides valuable insights into identifying individuals suitable for isolation release based on SARS-CoV-2 testing in Japan.

Lyophilized nasal swabs for COVID-19 detection by ATR-FTIR spectroscopy: Machine learning-based approach

The COVID-19 pandemic continues to pose challenges for global health. The disease burden and diagnostic pressure has forced scientists to explore alternate diagnostic tools beyond the standard PCR testing. One such promising tool is the use of spectroscopy-based diagnostics. The objective of this study is to assess the potential of ATR-FTIR spectroscopy, applied to lyophilized nasal swab samples to discriminate between healthy and infected COVID-19 patients. Equal number (55 each) of positive and negative freeze-dried nasal swab samples were analyzed. After pre-processing, average mean spectra (600-4000 cm-1) showed significant variations between healthy and infected sample types. Clear spectral variations were recorded at 17 locations, of which, 13 peaks were observed in COVID-19 spectra while 4 peaks were observed in negative sample spectra. Statistical discrimination was done using principal component analysis (PCA), linear discriminant analysis (LDA) and support vector machine (SVM). The first two principal components (PCs) showed a combined variance of 76 %. Classification accuracy of 100 % were observed in the LDA graph using Quadratic kernel. Similarly, SVM model with both internal validation and external validation confirmed the robustness with a 100 % classification accuracy. These results show that lyophilized nasal swab samples are the ideal sample choice for FTIR-based analysis of COVID-19. This sample preparation method coupled with spectroscopy can serve as a robust and accessible diagnostic tool for post-covid testing.

What drives the effectiveness of social distancing in combating COVID-19 across U.S. states?

We propose a new theory of information-based voluntary social distancing in which people's responses to disease prevalence depend on the credibility of reported cases and fatalities and vary locally. We embed this theory into a new pandemic prediction and policy analysis framework that blends compartmental epidemiological/economic models with Machine Learning. We find that lockdown effectiveness varies widely across US States during the early phases of the COVID-19 pandemic. We find that voluntary social distancing is higher in more informed states, and increasing information could have substantially changed social distancing and fatalities.

A Systematic Review of Prolonged SARS-CoV-2 Shedding in Immunocompromised Persons

BACKGROUND

Although reports have documented prolonged SARS-CoV-2 RNA detection in immunocompromised patients, few studies have systematically analyzed data on duration of SARS-CoV-2 in respiratory specimens of immunocompromised patients.

METHODS

A systematic review was undertaken to describe SARS-CoV-2 RNA and infectious virus detection in immunocompromised patients from published data between January 1, 2020 and July 1, 2022. Patients were included if there was ≥ 1 positive SARS-CoV-2 RNA result in respiratory specimens collected > 20 days since symptom onset or first positive SARS-CoV-2 RT-PCR result.

RESULTS

Of the 183 patients, 175 were symptomatic with 83 (47.4%) that experienced intermittent relapsing symptoms, while pneumonia was reported in 122 (66.7%). Immunocompromising conditions represented were hematologic malignancy treatment (89, 48.6%), solid organ transplant (47, 25.7%), autoimmune disease treatment (14, 7.7%), solid tumor treatment (3, 1.6%), HIV infection (15, 8.2%), and primary immunodeficiency (15, 8.2%). Median duration from the first to the last positive SARS-CoV-2 RT-PCR result was 56 days in upper respiratory and 60 days in lower respiratory tract specimens. Significant differences in median duration of SARS-CoV-2 RNA detection were observed between patients with and without pneumonia and for patients with hematologic malignancies compared to solid organ transplant patients. Among patients with viral culture performed, median duration of replication-competent SARS-CoV-2 was 60.5 days from symptom onset (maximum 238 days) and 59 days from first RT-PCR positive result (maximum 268 days).

CONCLUSIONS

Immunocompromised persons can have replication-competent SARS-CoV-2 in respiratory tissues for months, including while asymptomatic. Serial SARS-CoV-2 testing can inform the duration of isolation for immunocompromised patients with SARS-CoV-2 infection.

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Pathogen genomics can provide insights into underlying infectious disease transmission patterns1,2, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential3-5. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences to characterize fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that the location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postcodes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this study improves our ability to use large pathogen genome datasets to understand the determinants of infectious disease spread.

Age- and vaccination status-dependent isolation guidelines based on simulation of SARS-CoV-2 Delta cases in Singapore

BACKGROUND

In the absence of effective pharmaceutical interventions early in an infectious disease outbreak, non-pharmaceutical measures, especially isolating infected individuals, critically limit its impact. The ongoing COVID-19 pandemic has sparked debates on optimal isolation guidelines. This study proposes a variable isolation period approach (variable-period approach), tailoring isolation durations for distinct population groups with varied viral load dynamics.

METHODS

To compare our variable-period approach with a fixed-period strategy, we developed a simulation model generating synthetic longitudinal SARS-CoV-2 viral load data. The data was generated from the viral dynamics model parameterized using SARS-CoV-2 Delta patient data in Singapore, accounting for age and vaccination status.

RESULTS

Findings show that age and vaccination status significantly influence viral dynamics, with younger age and vaccination linked to shorter viral shedding durations. The variable-period framework suggests longer isolation lengths for older and unvaccinated individuals. By setting the leaking risk (risk of remaining infectious at the end of isolation) below 10%, the optimal fixed-period isolation is 14 days, with an average excess isolation burden of 7.4 unnecessary days. In contrast, the variable-period guideline reduces the excess isolation burden to 6.0 days, with the optimal isolation periods ranging from 9 to 16 days, depending on the population group. We confirmed similar results when we used the effective reproduction number as an alternative to the leaking risk.

CONCLUSIONS

In this case, study using the SARS-CoV-2 Delta variant, our analysis demonstrates that unnecessary time spent in isolation can be reduced by adopting variable-period guidelines based on patient characteristics.

Point-Of-Need One-Pot Multiplexed RT-LAMP Test For Detecting Three Common Respiratory Viruses In Saliva

Respiratory viral infections pose a significant global public health challenge, partly due to the difficulty in rapidly and accurately distinguishing between viruses with similar symptoms at the point of care, hindering timely and appropriate treatment and limiting effective infection control and prevention efforts. Here, we developed a multiplexed, non- invasive saliva-based, reverse transcription loop-mediated isothermal amplification (RT- LAMP) test that enables the simultaneous detection of three of the most common respiratory infections, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Influenza (Flu), and respiratory syncytial virus (RSV), in a single reaction via specific probes and monitored in real-time by a machine-learning-enabled compact analyzer. Our results demonstrate that the multiplexed assay can effectively detect three target RNAs with high accuracy. Further, testing with spiked saliva samples showed strong agreement with reverse transcription polymerase chain reaction (RT-PCR) assay, with area under the curve (AUC) values of 0.82, 0.93, and 0.96 for RSV, Influenza, and SARS-CoV-2, respectively. By enabling the rapid detection of respiratory infections from easily collected saliva samples at the point of care, the device presented here offers a practical and efficient tool for improving outcomes and helping prevent the spread of contagious diseases.

Significance

This research presents an innovative approach to respiratory infection diagnostics by combining a one-pot isothermal molecular test with machine learning-based analysis to simultaneously detect SARS-CoV-2, Influenza, and RSV in saliva samples. The battery- powered portable analyzer features novel machine-learning-assisted fluorescence detection for multiplexed reporter quantification, eliminating the need for traditional filter- based optical components and enabling adaptation to new targets without hardware changes. The test demonstrates high accuracy in detecting single and co-infections in spiked saliva samples, providing a rapid, cost-effective point-of-need solution. This tool can expand testing access, improve patient outcomes, and support more effective disease control, particularly in resource-limited or decentralized healthcare settings.

Clinical performance of Abbott ID NOW™ COVID-19 2.0 rapid molecular point-of-care test compared to three real-time RT-PCR assays

Timely diagnosis of SARS-CoV-2 is important for infection control and treatment. Real-time reverse transcriptase PCR (rRT-PCR) tests are the reference standard for diagnosis but often require a centralized laboratory, making them time-intensive and unsuitable for resource-limited settings. The Abbott ID NOW™ COVID-19 2.0 assay is a rapid point-of-care (POC), isothermal molecular test for qualitative detection of SARS-CoV-2. We prospectively evaluated its clinical performance against three reference rRT-PCR tests: Hologic Panther Fusion, Roche Cobas, and CDC 2019-nCoV RT-PCR Diagnostic Panel. Investigators enrolled 3,530 subjects, with 3,146 evaluable. In symptomatic subjects (n = 914), the test showed a positive percent agreement (PPA) of 91.7% (95% confidence interval [CI]: 87.8, 94.4) and a negative percent agreement (NPA) of 98.4% (95% CI: 97.1, 99.1). The PPA improved with lower cycle threshold (Ct) values: 94.7% (95% CI: 91.2, 97.2) for Ct ≤36, 97.6% (95% CI: 94.5, 99.2) for Ct ≤33, and 99.4% (95% CI: 96.8, 100.0) for Ct ≤30. Discordant results were observed among the three reference rRT-PCR tests across evaluable subjects with suspected COVID-19 infection. For 1,630 cases of symptomatic and asymptomatic subjects suspected of COVID-19, where all three rRT-PCR methods were evaluable, CDC test results differed the most, with 144 discordant results with Roche and 119 with Panther rRT-PCR tests. Roche and Panther test results differed in 67 cases. In summary, the Abbott ID NOW™ COVID-19 2.0 assay can serve as a valuable diagnostic tool in acute symptomatic subjects in point-of-care settings.

IMPORTANCE

The Abbott ID NOWTM COVID-19 2.0 assay is a suitable rapid test for diagnosing COVID-19 in acute symptomatic subjects and can be used in point-of-care settings and low-resource settings. With results reported in 12 minutes or less, Abbott ID NOWTM COVID-19 2.0 facilitates timely diagnosis, enabling linkage to appropriate antiviral medication.

Assessment of COVID-19 incidence after performing pulmonary function tests during the pandemic: Findings from a real-life cohort

BACKGROUND

Pulmonary function testing (PFT) is paramount in assessing patients with respiratory symptoms and chronic cardiopulmonary diseases. Although seminal studies have demonstrated that PFT generates aerosols, this simple observation does not confirm the potential for enhanced pathogen transmission.

OBJECTIVE

We aimed to describe the frequency of patients who developed suspected symptoms of COVID-19, prompting SARS-CoV-2 testing after undergoing PFT during the reopening of a laboratory amid the deceleration of the pandemic.

METHODS

We analyzed a retrospective cohort of individuals referred for PFT between May and August 2021. Two weeks post-PFT, phone calls were made asking about suspected symptoms of COVID-19, leading to SARS-CoV-2 testing. The medical data of the participants who did not answer the phone calls were reviewed through institutional electronic records. The minimum sample size of 338 individuals was calculated to detect an incidence of COVID-19 at least ten times higher than the surrounding local rate (0.08 %).

RESULTS

Three hundred and sixty patients (40.6 % men; 56.5 ± 17.6 years) were included. PFT was primarily indicated for functional and prognostic assessments of chronic respiratory diseases. Three hundred and sixteen patients answered the follow-up phone calls. Following PFT, most patients (357/360) did not report suspected symptoms leading to COVID-19 confirmation testing. Three patients underwent RT-PCR testing, which yielded negative results.

CONCLUSION

Patients in this real-life cohort, after performing PFT, did not experience an outbreak (with a rate of at least ten times the surrounding local rate) or a cluster (with two or more cases) of symptomatic COVID-19.

Post-exposure testing at healthcare facilities with SARS-CoV-2 transmission: A rapid review

Background

Post-exposure severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing following health facility outbreaks may control the spread of infection.

Aim

This study aimed to assess the impact of testing for SARS-CoV-2 infection on health outcomes during healthcare facility outbreaks.

Setting

This review included studies conducted at skilled nursing facilities, a cancer centre, and a geriatric psychiatric facility.

Methods

We followed the methods for conducting rapid systematic reviews, searched databases from December 2019 to August 2022, assessed the risk of bias using the modified Newcastle Ottawa scale, and graded the certainty of evidence using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) approach. We pooled the prevalence, mortality, and hospitalisation results as appropriate.

Results

Of the 3055 articles from database search, no study was eligible for inclusion as outlined in the protocol. However, eight non-comparative reports (case series) in skilled nursing facilities were included. The pooled prevalence of SARS-CoV-2 infection among residents of care homes and patients were 38% (95% confidence interval [CI] = 25% - 51%; 5 studies, 2044 participants; I 2 = 94%, very low certainty evidence) and was 12% (95% CI = 6% - 19%; 5 studies, 2312 participants; I 2 = 94%, very low certainty evidence) for exposed healthcare workers. The pooled mortality estimate and hospitalisation rate were 17% and 24%, respectively, (very low certainty evidence).

Conclusion

There is no identified evidence for or against testing of people in healthcare facilities where there is ongoing transmission of SARS-CoV-2 infection.

Contribution

The evaluation of the effectiveness of testing strategies during SARS-CoV-2 outbreaks need baseline and follow-up data from well-designed before and after studies appropriate for the setting.

SARS-CoV-2 infection rates and associated risk factors in healthcare workers: systematic review and meta-analysis

To protect healthcare workforce during the COVID-19 pandemic, rigorous efforts were made to reduce infection rates among healthcare workers (HCWs), especially prior to vaccine availability. This study aimed to investigate the prevalence of SARS-CoV-2 infections among HCWs and identify potential risk factors associated with transmission. We searched MEDLINE, Embase, and Google Scholar from 1 December 2019 to 5 February 2024. From 498 initial records, 190 articles were reviewed, and 63 studies were eligible. ROBINS-E tool revealed a lower risk of bias in several domains; however, some concerns related to confounding and exposure measurement were identified. Globally, 11% (95% confidence interval (CI) 9-13) of 283,932 HCWs were infected with SARS-CoV-2. Infection rates were associated with a constellation of risk factors and major circulating SARS-CoV-2 variants. Household exposure (odds ratio (OR) 7.07; 95% CI 3.93-12.73), working as a cleaner (OR 2.72; 95% CI 1.39-5.32), occupational exposure (OR 1.79; 95% CI 1.49-2.14), inadequate training on infection prevention and control (OR 1.46; 95% CI 1.14-1.87), insufficient use of personal protective equipment (OR 1.45; 95% CI 1.14-1.84), performing aerosol generating procedures (OR 1.36; 95% CI 1.21-1.52) and inadequate hand hygiene (OR 1.17; 95% CI 0.79-1.73) were associated with an increased SARS-CoV-2 infection. Conversely, history of quarantine (OR 0.23; 95% CI 0.08-0.60) and frequent decontamination of high touch areas (OR 0.52; 95% CI 0.42-0.64) were protective factors against SARS-CoV-2 infection. This study quantifies the substantial global burden of SARS-CoV-2 infection among HCWs. We underscore the urgent need for effective infection prevention and control measures, particularly addressing factors such as household exposure and occupational practices by HCWs, including cleaning staff.

High-frequency PCR-testing as a powerful approach for SARS-CoV-2 surveillance in the field of critical infrastructure: A longitudinal, retrospective study in a German tertiary care hospital

A high number of SARS-CoV-2 infections are mild, often even asymptomatic. Because of high specificity and sensitivity, RT-PCR is considered the gold-standard for COVID-19 testing. The technology played a key role in detecting sources of infection at an early stage and therefore preventing larger outbreaks. This was especially important in case of critical infrastructure, such as hospitals. Until now, comprehensive studies concerning the impact of high-frequency PCR-testing in German tertiary care hospitals during the COVID-19 pandemic are lacking. We therefore analyzed about 285.000 oral swab probes of 3.421 healthcare-workers concerning SARS-CoV-2 RNA positivity between November 2020 and February 2023. Our data show that frequent PCR-testing is a useful tool concerning SARS-CoV-2 surveillance. Due to the longitudinal character of the study, we were able to observe SARS-CoV-2 variant-specific differences. For example, the omicron-variant led to high reinfection-rates as well as lower Ct-values. Nevertheless, reinfection rates in our hospital are much lower compared to other analyzed healthcare-worker cohorts described in the literature, which is again attributable to the frequent testing-regime implemented in the early phase of the pandemic. Our data further reveal a longer infection-duration in elderly compared to younger individuals.

Significance of supervision sampling in control of communicable respiratory disease simulated by a new model during different stages of the disease

The coronavirus disease 2019 (COVID-19) interventions in interrupting transmission have paid heavy losses politically and economically. The Chinese government has replaced scaling up testing with monitoring focus groups and randomly supervising sampling, encouraging scientific research on the COVID-19 transmission curve to be confirmed by constructing epidemiological models, which include statistical models, computer simulations, mathematical illustrations of the pathogen and its effects, and several other methodologies. Although predicting and forecasting the propagation of COVID-19 are valuable, they nevertheless present an enormous challenge. This paper emphasis on pandemic simulation models by introduced respiratory-specific transmission to extend and complement the classical Susceptible-Exposed-(Asymptomatic)-Infected-Recovered SE(A)IR model to assess the significance of the COVID-19 transmission control features to provide an explanation of the rationale for the government policy. A novel epidemiological model is developed using mean-field theory. Utilizing the SE(A)IR extended framework, which is a suitable method for describing the progression of epidemics over actual or genuine landscapes, we have developed a novel model named SEIAPUFR. This model effectively detects the connections between various stages of infection. Subsequently, we formulated eight ordinary differential equations that precisely depict the population's temporal development inside each segment. Furthermore, we calibrated the transmission and clearance rates by considering the impact of various control strategies on the epidemiological dynamics, which we used to project the future course of COVID-19. Based on these parameter values, our emphasis was on determining the criteria for stabilizing the disease-free equilibrium (DEF). We also developed model parameters that are appropriate for COVID-19 outbreaks, taking into account varied population sizes. Ultimately, we conducted simulations and predictions for other prominent cities in China, such as Wuhan, Shanghai, Guangzhou, and Shenzhen, that have recently been affected by the COVID-19 outbreak. By integrating different control measures, respiratory-specific modeling, and disease supervision sampling into an expanded SEI (A) R epidemic model, we found that supervision sampling can improve early warning of viral activity levels and superspreading events, and explained the significance of containments in controlling COVID-19 transmission and the rationality of policy by the influence of different containment measures on the transmission rate. These results indicate that the control measures during the pandemic interrupted the transmission chain mainly by inhibiting respiratory transmission, and the proportion of supervision sampling should be proportional to the transmission rate, especially only aimed at preventing a resurgence of SARS-CoV-2 transmission in low-prevalence areas. Furthermore, The incidence hazard of Males and Females was 1.39(1.23-1.58), and 1.43(1.26-1.63), respectively. Our investigation found that the ratio of peak sampling is directly related to the transmission rate, and both decrease when control measures are implemented. Consequently, the control measures during the pandemic interrupted the transmission chain mainly by inhibiting respiratory transmission. Reasonable and effective interventions during the early stage can flatten the transmission curve, which will slow the momentum of the outbreak to reduce medical pressure.

A modeling study to define guidelines for antigen screening in schools and workplaces to mitigate COVID-19 outbreaks

BACKGROUND

In-person interaction offers invaluable benefits to people. To guarantee safe in-person activities during a COVID-19 outbreak, effective identification of infectious individuals is essential. In this study, we aim to analyze the impact of screening with antigen tests in schools and workplaces on identifying COVID-19 infections.

METHODS

We assess the effectiveness of various screening test strategies with antigen tests in schools and workplaces through quantitative simulations. The primary outcome of our analyses is the proportion of infected individuals identified. The transmission process at the population level is modeled using a deterministic compartmental model. Infected individuals are identified through screening tests or symptom development. The time-varying sensitivity of antigen tests and infectiousness is determined by a viral dynamics model. Screening test strategies are characterized by the screening schedule, sensitivity of antigen tests, screening duration, timing of screening initiation, and available tests per person.

RESULTS

Here, we show that early and frequent screening is the key to maximizing the effectiveness of the screening program. For example, 44.5% (95% CI: 40.8-47.5) of infected individuals are identified by daily testing, whereas it is only 33.7% (95% CI: 30.5-37.3) when testing is performed at the end of the program duration. If high sensitivity antigen tests (Detection limit: 6.3 × 10 4 copies/mL) are deployed, it reaches 69.3% (95% CI: 66.5-72.5).

CONCLUSIONS

High sensitivity antigen tests, high frequency screening tests, and immediate initiation of screening tests are important to safely restart educational and economic activities in-person. Our computational framework is useful for assessing screening programs by incorporating situation-specific factors.

What Can We Learn for Future Integrated Care Models in Long Term Care Facilities After the COVID-19 Emergency? Lessons From an Observational Study in Catalonia

Introduction

The healthcare response to the COVID-19 pandemic in long term care facilities (LTCF), constitutes one of the challenges faced by governments and institutions worldwide. Our aim was to analyze the facilitators and barriers of this response, for the future integrated care model in these facilities.

Methods

From a retrospective observational study, we present the experience and lessons learned of the implementation of an integrated response at the meso level in LTCF for older people and for people with physical and mental conditions in the North Metropolitan area of Barcelona, in Catalonia, during the COVID-19 pandemic.

Results

We analyzed the care provided to 13,369 institutionalized people. The major facilitating points were: the adaptation of proactive care teams, the creation of a tool to improve communication with institutions, and the management of epidemiological data for planning collaboration between different actors. Main barriers were not including users and family members views in the response adaptation, and the lack of LTCF resources to respond to changing needs.

Conclusions

Increasing proactivity and adapting interventions based on updated information were key to minimize infections and mortality. Improving the communication and the collaboration between actors, and people involvement in the response planning, need to be considered for the future.

A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are a continuous threat to human life. An urgent need remains for simple and fast tests that reliably detect active infections with SARS-CoV-2 and its variants in the early stage of infection. Here we introduce a simple and rapid activity-based diagnostic (ABDx) test that identifies SARS-CoV-2 infections by measuring the activity of a viral enzyme, Papain-Like protease (PLpro). The test system consists of a peptide that fluoresces when cleaved by SARS PLpro that is active in crude, unprocessed lysates from human tongue scrapes and saliva. Test results are obtained in 30 minutes or less using widely available fluorescence plate readers, or a battery-operated portable instrument for on-site testing. Proof-of-concept was obtained in a study on clinical specimens collected from patients with COVID-19 like symptoms who tested positive (n = 10) or negative (n = 10) with LIAT RT-PCR using nasal mid turbinate swabs. When saliva from these patients was tested with in-house endpoint RT-PCR, 17 were positive and only 5 specimens were negative, of which 2 became positive when tested 5 days later. PLpro activity correlated in 17 of these cases (3 out of 3 negatives and 14 out of 16 positives, with one invalid specimen). Despite the small number of samples, the agreement was significant (p value = 0.01). Two false negatives were detected, one from a sample with a late Ct value of 35 in diagnostic RT-PCR, indicating that an active infection was no longer present. The PLpro assay is easily scalable and expected to detect all viable SARS-CoV-2 variants, making it attractive as a screening and surveillance tool. Additionally, we show feasibility of the platform as a new homogeneous phenotypic assay for rapid screening of SARS-CoV-2 antiviral drugs and neutralizing antibodies.

Association of Single-Nucleotide Variants in ACE2 with the Persistence of Positive qPCR Test for SARS-CoV-2 in Healthcare Professionals During the First Wave of the COVID-19 Pandemic

The persistence of qPCR positivity for SARS-CoV-2 in individuals who recovered from COVID-19 raised several questions regarding viral transmission, with a special interest in healthcare professionals who may pose a risk of transmitting SARS-CoV-2. This issue highlights the necessity for identifying the genetic risk factors associated with persistent SARS-CoV-2 infection. A promising target for achieving this goal is the angiotensin-converting enzyme 2 (ACE2) gene, which has been associated with clinical characteristics of COVID-19 infection, such as severity. The analysis of samples from the first wave of the COVID-19 pandemic represents the initial response of the immune human system against this new virus, without the effect of vaccination or the presence of multiple strains. The aim of this study was to analyze the association of genetic variants in ACE2 with persistent SARS-CoV-2 infection. We conducted a case-control study, including 151 healthcare workers who tested positive for SARS-CoV-2 by qPCR during the first wave of the COVID-19 pandemic, and who were followed up until their results were negative. ACE2 was sequenced through Sanger sequencing. The sequence was compared against a reference sequence and variants identified. Four ACE2 variants were associated with persistent SARS-CoV-2 qPCR positivity. Three of the variants with an effect on the resulting protein were associated with increased risk of persistent SARS-CoV-2 qPCR positivity, NG_012575.2:g.35481 C>T, NG_012575.2:g.35483 G>T and NG_012575.2:g.35498 G>T. On the other hand, the rs2285666 (NG_012575.2:g.14934 G>A) was associated with a higher risk for persistent SARS-CoV-2 qPCR positivity in women and rs4646150 (NG_012575.2:g.25701 G>A) in men. The NG_012575.2:g.35498 G>T variant represents an amino acid change with a possibly harmful effect on ACE2 function. Our results suggest that ACE2 variants might be useful for identifying the population at higher risk for developing persistent SARS-CoV-2-positive qPCR results. This knowledge can be helpful for designing health policies for protecting healthcare professionals and, in consequence, users of health services.

The effectiveness of interventions to reduce the transmission of acute respiratory infections in care homes: a systematic review

BACKGROUND

Care home residents are at high risk from outbreaks of respiratory infections, such as influenza and COVID-19. We conducted a systematic review of randomized controlled trials, to determine which interventions (apart from vaccines) are effective at reducing transmission of acute respiratory illnesses (ARIs) in care homes.

METHODS

We searched CINAHL, Medline, Embase and Cochrane for randomized controlled trials (RCTs) of interventions to prevent transmission of ARIs in care homes (excluding vaccines), to April 2023.

RESULTS

A total of 21 articles met inclusion criteria. Two infection control interventions significantly reduced respiratory infections. Oseltamivir significantly reduced risk of symptomatic laboratory-confirmed influenza (OR 0.39, 95%CI 0.16-0.94, three trials), and influenza-like illness (OR 0.50, 95%CI 0.36-0.69), even in a vaccinated population. High dose vitamin D supplementation reduced incidence of ARIs (incidence rate ratio 0.60; 95%CI 0.38-0.94, one trial). Nine other RCTs of vitamin, mineral, probiotic and herbal supplements showed no significant effect.

CONCLUSION

Transmission of respiratory infections in care homes can be reduced by educational interventions to improve infection control procedures and compliance by staff, by antiviral prophylaxis soon after a case of influenza has been detected, and by supplementation with high-dose Vitamin D3. Further research is needed to confirm the effect of high-dose Vitamin D3.

Detection of SARS-CoV-2 in wastewater as an earlier predictor of COVID-19 epidemic peaks in Venezuela

Wastewater-based epidemiological surveillance has proven to be a useful and cost-effective tool for detecting COVID-19 outbreaks. Here, our objective was to evaluate its potential as an early warning system in Venezuela by detecting SARS-CoV-2 RNA in wastewater and its correlation with reported cases of COVID-19. Viral RNA was concentrated from wastewater collected at various sites in Caracas (northern Venezuela), from September 2021 to July 2023, using the polyethylene glycol (PEG) precipitation method. Viral quantification was performed by RT-qPCR targeting the N1 and ORF1ab genes. A significant association (p < 0.05) was found between viral load in wastewater and reported cases of COVID-19 up to six days after sampling. During the whole study, two populated areas of the city were persistent hotspots of viral infection. The L452R mutation, suggestive of the presence of the Delta variant, was identified in the only sample where a complete genomic sequence could be obtained. Significant differences (p < 0.05) between the physicochemical conditions of the wastewater samples positive and negative for the virus were found. Our results support proof of concept that wastewater surveillance can serve as an early warning system for SARS-CoV-2 outbreaks, complementing public health surveillance in those regions where COVID-19 is currently underreported.

Improved efficacy of SARS-CoV-2 isolation from COVID-19 clinical specimens using VeroE6 cells overexpressing TMPRSS2 and human ACE2

The cell culture-based isolation of novel coronavirus SARS-CoV-2 from clinical specimens obtained from patients with suspected COVID-19 is important not only for laboratory diagnosis but also for obtaining live virus to characterize emerging variants. Previous studies report that monkey kidney-derived VeroE6/TMPRSS2 cells allow efficient isolation of SARS-CoV-2 from clinical specimens because these cells show stable expression of the receptor molecule monkey ACE2 and the serine-protease TMPRSS2. Here, we demonstrated that VeroE6 cells overexpressing human ACE2 and TMPRSS2 (Vero E6-TMPRSS2-T2A-ACE2 cells) are superior to VeroE6/TMPRSS2 for isolating SARS-CoV-2 from clinical specimens. These cells showed a 1.6-fold increase in efficiency in SARS-CoV-2 isolation, and were particularly effective for clinical specimens with a relatively low viral load (< 106 copies/mL). When using vesicular stomatitis virus (VSV) pseudoviruses (VSV/SARS-2pv) bearing the spike proteins of all of the tested SARS-CoV-2 strains, Vero E6-TMPRSS2-T2A-ACE2 cells showed a 2- to fourfold increase in infectivity. Furthermore, the results of virus titration and neutralization antibody assays using Vero E6-TMPRSS2-T2A-ACE2 cells were different from those using VeroE6/TMPRSS2, highlighting the importance of selecting appropriate cell culture systems to determine SARS-CoV-2 infectivity.

Cycle Threshold Values of SARS-CoV-2 RT-PCR during Outbreaks in Nursing Homes: A Retrospective Cohort Study

Backgound/Objectives: Cycle threshold (Ct) values of SARS-CoV-2 real-time reverse transcriptase-polymerase chain reaction (RT-PCR) tests are associated with infectivity and viral load, and they could be an aid in forecasting the evolution of SARS-CoV-2 outbreaks. The objective was to know the Ct values related to the incidence and reinfection of SARS-CoV-2 in successive outbreaks, which took place in nursing homes in Castellon (Spain) during 2020-2022, and to test its usefulness as an instrument of epidemic surveillance in nursing homes.

METHODS

a retrospective cohort design with Poisson regression and multinomial logistic regression were used.

RESULTS

We studied four nursing home SARS-CoV-2 outbreaks, and the average infection rate, reinfection rate, and case fatality were 72.7%, 19.9%, and 5.5%, respectively; 98.9% of residents were vaccinated with three doses of a mRNA SARS-CoV-2 vaccine. Ct values for first infections and reinfections were 27.1 ± 6.6 and 31.9 ± 5.4 (p = 0.000). Considering Ct values ≥ 30 versus <30, residents with reinfections had Ct values higher than residents with a first infection, an adjusted relative risk of 1.66 (95% Confidence interval 1.10-2.51). A sensitivity analysis confirmed these results.

CONCLUSIONS

Reinfection and SARS-CoV-2 vaccination (hybrid immunity) could protect against severe disease better than vaccination alone. High Ct values suggest lower transmission and severity. Its value can be useful for surveillance and forecasting future SARS-CoV-2 epidemics.

SARS-CoV-2 Seropositivity in Nursing Home Staff and Residents during the First SARS-CoV-2 Wave in Flanders, Belgium

(1) Background: early in the COVID-19 pandemic, reverse transcription polymerase chain reaction (RT-PCR) testing was limited. Assessing seroprevalence helps understand prevalence and reinfection risk. However, such data are lacking for the first epidemic wave in Belgian nursing homes. Therefore, we assessed SARS-CoV-2 seroprevalence and cumulative RT-PCR positivity in Belgian nursing homes and evaluated reinfection risk. (2) Methods: we performed a cross-sectional study in nine nursing homes in April and May 2020. Odds ratios (ORs) were calculated to compare the odds of (re)infection between seropositive and seronegative participants. (3) Results: seroprevalence was 21% (95% CI: 18-23): 22% (95% CI: 18-25) in residents and 20% (95% CI: 17-24) in staff. By 20 May 2020, cumulative RT-PCR positivity was 16% (95% CI: 13-21) in residents and 8% (95% CI: 6-12) in staff. ORs for (re)infection in seropositive (compared to seronegative) residents and staff were 0.22 (95% CI: 0.06-0.72) and 3.15 (95% CI: 1.56-6.63), respectively. (4) Conclusion: during the first wave, RT-PCR test programmes underestimated the number of COVID-19 cases. The reinfection rate in residents was 3%, indicating protection, while it was 21% in staff, potentially due to less cautious health behaviour. Future outbreaks should use both RT-PCR and serological testing for complementary insights into transmission dynamics.

Longitudinal fecal shedding of SARS-CoV-2, pepper mild mottle virus, and human mitochondrial DNA in COVID-19 patients

Since the coronavirus disease 2019 (COVID-19) pandemic, wastewater-based epidemiology (WBE) has been widely applied in many countries and regions for monitoring COVID-19 transmission in the population through testing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. However, the amount of virus shed by individuals over time based on the stage of infection and accurate number of infections in the community creates challenges in predicting COVID-19 prevalence in the population and interpreting WBE results. In this study, we measured SARS-CoV-2, pepper mild mottle virus (PMMoV), and human mitochondrial DNA (mtDNA) in longitudinal fecal samples collected from 42 COVID-19 patients for up to 42 days after diagnosis. SARS-CoV-2 RNA was detected in 73.1% (19/26) of inpatient study participants in at least one of the collected fecal specimens during the sampling period. Most participants shed the virus within 3 weeks after diagnosis, but five inpatient participants still shed the virus between 20 and 60 days after diagnosis. The median concentration of SARS-CoV-2 in positive fecal samples was 1.08 × 105 genome copies (GC)/gram dry fecal material. PMMoV and mtDNA were detected in 99.4% (154/155) and 100% (155/155) of all fecal samples, respectively. The median concentrations of PMMoV RNA and mtDNA in fecal samples were 1.73 × 107 and 2.49 × 108 GC/dry gram, respectively. These results provide important information about the dynamics of fecal shedding of SARS-CoV-2 and two human fecal indicators in COVID-19 patients. mtDNA showed higher positive rates, higher concentrations, and less variability between and within individuals than PMMoV, suggesting that mtDNA could be a better normalization factor for WBE results than PMMoV.

ƩS COVID-19 is a rapid high throughput and sensitive one-step quadruplex real-time RT-PCR assay

Real-time reverse transcription polymerase chain reaction (RT-PCR), a standard method recommended for the diagnosis of coronavirus disease 2019 (COVID-19) requires 2-4 h to get the result. Although antigen test kit (ATK) is used for COVID-19 screening within 15-30 min, the drawback is its limited sensitivity. Hence, a rapid one-step quadruplex real-time RT-PCR assay: termed ƩS COVID-19 targeting ORF1ab, ORF3a, and N genes of SARS-CoV-2; and Avocado sunblotch viroid (ASBVd) as an internal control was developed. Based on strategies including designing high melting temperature primers with short amplicons, applying a fast ramp rate, minimizing hold time, and reducing the range between denaturation and annealing/extension temperatures; the assay could be accomplished within 25 min. The limit of detection of ORF1ab, ORF3a, and N genes were 1.835, 1.310, and 1 copy/reaction, respectively. Validation was performed in 205 combined nasopharyngeal and oropharyngeal swabs. The sensitivity, specificity, positive predictive value, and negative predictive value were 92.8%, 100%, 100%, and 97.1%, respectively with 96.7% accuracy. Cohen's Kappa was 0.93. The newly developed rapid real-time RT-PCR assay was highly sensitive, specific, and fast, making it suitable for use as an alternative method to support laboratory diagnosis of COVID-19 in outpatient and emergency departments.

Data-driven mathematical modeling approaches for COVID-19: A survey

In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure. Eventually, we review the literature, based on 260 articles selected in 11 sections, ranging from the medical survey of hospital cases to forecasting the dynamics of new cases in the general population. This review favors the phenomenological approach over the mechanistic approach in the choice of references and provides simulations of the evolution of the number of observed cases of COVID-19 for 10 states (California, China, France, India, Israel, Japan, New York, Peru, Spain and United Kingdom).

A visualized and bibliometric analysis of nursing research during the COVID-19 pandemic

BACKGROUND

The global spread of Coronavirus disease 2019 (COVID-19) has been increasing since December 2019. A total of 8460 publications were obtained from the Web of Science Core Collection from 2019 to 2023, providing insights into the progress of nursing research throughout the COVID-19 pandemic.

METHODS

Bibliometric analysis was conducted on these articles using CiteSpace. The analysis focused on examining the distribution of these publications in terms of space and time, distribution of authors, subject categories, distribution of topics, and cited references.

RESULTS

These results may be explained from 3 perspectives. Initially, the number of yearly publications on nursing research consistently increased during the COVID-19 pandemic. Furthermore, a co-occurrence analysis of the countries and the authors revealed that certain countries, including the United States, China, and England, have successfully implemented organized and standardized nursing models. These countries also have well-developed and established nursing research systems. Notably, academic communities in specific regions, such as the team led by MD Stefan Gravenstein, Mor Vincent, and White Elizabeth at Brown University in the United States, have emerged as leaders in this field. Furthermore, examining the papers' subject categories and topic distribution indicate that nursing during the COVID-19 pandemic has been predominantly interdisciplinary, encompassing various disciplines such as clinical medicine, essential medicine, psychology, public health management, and even telematics science.

CONCLUSION SUBSECTIONGS

Our study provided valuable insights into acquiring knowledge on nursing research during the COVID-19 pandemic, pinpointed possible partners for researchers interested in nursing, and uncovered prevalent research patterns and popular subjects.

Opportunities for Enhanced Public Health Surveillance via Molecular Detection and Sequencing of Diverse Respiratory Viruses From Self-collected SARS-CoV-2 Antigen Test Swabs

We sequenced and genotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, adenovirus, and respiratory syncytial virus, among other pathogens, from residual anterior nasal swabs self-collected for rapid SARS-CoV-2 antigen testing at the US Naval Academy. This is a key proof-of-concept for an acute respiratory infection surveillance approach, which could leverage prevalent SARS-CoV-2 antigen self-testing.

Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022

This study examines the epidemiological and genomic characteristics, along with the transmission dynamics, of SARS-CoV-2 within prison units I and II in Campo Grande, Mato Grosso do Sul, Brazil. Conducted between May and October 2022, it reveals how the virus spreads in the confined settings of prisons, emphasizing the roles of overcrowded cells, frequent transfers, and limited healthcare access. The research involved 1927 participants (83.93% of the total prison population) and utilized nasopharyngeal swabs and RT-qPCR testing for detection. Contact tracing monitored exposure within cells. Out of 2108 samples, 66 positive cases were identified (3.13%), mostly asymptomatic (77.27%), with the majority aged 21-29 and varying vaccination statuses. Next-generation sequencing generated 28 whole genome sequences, identifying the Omicron variant (subtypes BA.2 and BA.5) with 99% average coverage. Additionally, the study seeks to determine the relationship between immunization levels and the incidence of SARS-CoV-2 cases within this enclosed population. The findings underscore the necessity of comprehensive control strategies in prisons, including rigorous screening, isolation protocols, vaccination, epidemiological monitoring, and genomic surveillance to mitigate disease transmission and protect both the incarcerated population and the broader community.

Secondary attack rate following on-site isolation of patients with suspected COVID-19 in multiple-bed rooms

The implementation of isolation precautions for patients with suspected Coronavirus Disease 2019 (COVID-19) and pending test results is resource intensive. Due to the limited availability of single-bed rooms at our institution, we isolated patients with suspected COVID-19 together with patients without suspected COVID-19 on-site in multiple-bed rooms until SARS-CoV-2-test results were available. We evaluated the likelihood of SARS-CoV-2 transmission to individuals sharing the room with patients isolated on-site. This observational study was performed at the University Hospital Basel, Switzerland, from 03/20 - 11/20. Secondary attack rates were compared between patients hospitalized in multiple-bed rooms and exposed to individuals subjected to on-site isolation precautions (on-site isolation group), and patients exposed to individuals initially not identified as having COVID-19, and not placed under isolation precautions until the diagnosis was suspected (control group). Transmission events were confirmed by whole-genome sequencing. Among 1,218 patients with suspected COVID-19, 67 (5.5%) tested positive for SARS-CoV-2. Of these, 21 were isolated on-site potentially exposing 27 patients sharing the same room. Median contact time was 12 h (interquartile range 7-18 h). SARS-CoV-2 transmission was identified in none of the patients in the on-site isolation group vs. 10/63 (15.9%) in the control group (p = 0.03). Isolation on-site of suspected COVID-19-patients in multiple-bed rooms avoided single-room occupancy and subsequent in-hospital relocation for many patients without confirmed SARS-CoV-2-infection. The absence of secondary transmission among the exposed patients in the on-site isolation group allows for assessment of the risk/benefit ratio of this strategy given the limitation of a small sample size.

Clinical Outcomes After Admission of Patients With COVID-19 to Skilled Nursing Facilities

Importance

During the COVID-19 pandemic, stabilized COVID-19-positive patients were discharged to skilled nursing facilities (SNFs) to alleviate hospital crowding. These discharges generated controversy due to fears of seeding outbreaks, but there is little empirical evidence to inform policy.

Objective

To assess the association between the admission to SNFs of COVID-19-positive patients and subsequent COVID-19 cases and death rates among residents.

Design, Setting, and Participants

This cohort study analyzed survey data from the National Healthcare Safety Network of the Centers for Disease Control and Prevention. The cohort included SNFs in the US from June 2020 to March 2021. Exposed facilities (ie, with initial admission of COVID-19-positive patients) were matched to control facilities (ie, without initial admission of COVID-19-positive patients) in the same county and with similar preadmission case counts. Data were analyzed from June 2023 to February 2024.

Exposure

The week of the first observable admission of COVID-19-positive patients (defined as those previously diagnosed with COVID-19 and continued to require transmission-based precautions) during the study period.

Main Outcomes and Measures

Weekly counts of new cases of COVID-19, COVID-19-related deaths, and all-cause deaths per 100 residents in the week prior to the initial admission. A stacked difference-in-differences approach was used to compare outcomes for 10 weeks before and 15 weeks after the first admission. Additional analyses examined whether outcomes differed in facilities with staff or personal protective equipment (PPE) shortages.

Results

A matched group of 264 exposed facilities and 518 control facilities was identified. Over the 15-week follow-up period, exposed SNFs had a cumulative increase of 6.94 (95% CI, 2.91-10.98) additional COVID-19 cases per 100 residents compared with control SNFs, a 31.3% increase compared with the sample mean (SD) of 22.2 (26.4). Exposed facilities experienced 2.31 (95% CI, 1.39-3.24) additional cumulative COVID-19-related deaths per 100 residents compared with control facilities, representing a 72.4% increase compared with the sample mean (SD) of 3.19 (5.5). Exposed facilities experiencing potential staff shortage and PPE shortage had larger increases in COVID-19 cases per 100 residents (additional 10.97 [95% CI, 2.76-19.19] cases and additional 14.81 [95% CI, 2.38-27.25] cases, respectively) compared with those without such shortages.

Conclusion

This cohort study suggests that admission of COVID-19-positive patients into SNFs early in the pandemic was associated with preventable COVID-19 cases and mortality among residents, particularly in facilities with potential staff and PPE shortages. The findings speak to the importance of equipping SNFs to adhere to infection-control best practices as they continue to face COVID-19 strains and other respiratory diseases.

Cutaneous manifestations associated with COVID-19 infection at a university hospital in eastern China

BACKGROUND

Coronavirus disease 2019 (COVID-19) affects different organ systems, including the skin. A retrospective analysis of skin manifestations in Chinese outpatient and inpatient settings is lacking. The study aims to analyze cutaneous manifestations in COVID-19 patients and the recurrence or aggravation of previous skin diseases.

MATERIALS AND METHODS

A retrospective cross-sectional study was conducted from November 2022 to July 2023 in a university hospital in eastern China. It involved reverse transcriptase polymerase chain reaction (RT-PCR)-positive COVID-19 patients, documenting various skin manifestations and the recurrence or aggravation of pre-existing skin conditions. The pattern of skin lesions and other variables were assessed.

RESULTS

The study included 303 patients, with 127 males and 176 females. Maculopapular rash was the predominant new cutaneous manifestation (54.92%), mainly in middle-aged individuals. Other findings included urticaria (16.39%), herpes zoster (11.89%), and herpes simplex (4.10%), vesicular rashes (2.46%), purpura (2.05%), erythema multiforme (1.64%), livedo reticularis (0.41%) and so on. Severe disease was associated with herpes zoster and livedo reticularis. Critical COVID-19 cases were linked to vesicular rashes, purpura, and erythema multiforme. The mean time for skin lesion emergence post-infection varied from 3 days for seborrheic dermatitis to 17.48 days for herpes zoster. Vasculitic manifestations correlated with elevated D-dimer levels. A total of 59 cases (19.47%) of recurrent or aggravated skin diseases were reported following infection with COVID-19, with dermatitis being the most common, followed by acne and folliculitis, psoriasis, urticaria, bullous pemphigoid, pemphigus, tinea corporis and androgenetic alopecia.

CONCLUSION

The cutaneous phenotypes delineated in this study expand the dermatologic spectrum associated with COVID-19. Cutaneous manifestations may result from overactive immune responses, complement activation, and microvascular damage. Herpes zoster typically occurs in elderly COVID-19 patients with weaker immune systems or more severe diseases. Purpura and livedo reticularis, although rare, may indicate disease severity. It is possible to predict the course of COVID-19 with different severity through cutaneous manifestations. Recognizing these skin manifestations could aid in predicting COVID-19 severity and guide dermatologists in managing the pandemic response.

No evidence for enhanced disease with human polyclonal SARS-CoV-2 antibody in the ferret model

Since SARS-CoV-2 emerged in late 2019, it spread from China to the rest of the world. An initial concern was the potential for vaccine- or antibody-dependent enhancement (ADE) of disease as had been reported with other coronaviruses. To evaluate this, we first developed a ferret model by exposing ferrets to SARS-CoV-2 by either mucosal inoculation (intranasal/oral/ocular) or inhalation using a small particle aerosol. Mucosal inoculation caused a mild fever and weight loss that resolved quickly; inoculation via either route resulted in virus shedding detected in the nares, throat, and rectum for 7-10 days post-infection. To evaluate the potential for ADE, we then inoculated groups of ferrets intravenously with 0.1, 0.5, or 1 mg/kg doses of a human polyclonal anti-SARS-CoV-2 IgG from hyper-immunized transchromosomic bovines (SAB-185). Twelve hours later, ferrets were challenged by mucosal inoculation with SARS-CoV-2. We found no significant differences in fever, weight loss, or viral shedding after infection between the three antibody groups or the controls. Signs of pathology in the lungs were noted in infected ferrets but no differences were found between control and antibody groups. The results of this study indicate that healthy, young adult ferrets of both sexes are a suitable model of mild COVID-19 and that low doses of specific IgG in SAB-185 are unlikely to enhance the disease caused by SARS-CoV-2.

An Evaluation of the Sensitivity and Specificity of Three COVID-19 Rapid Immunochromatographic Test Kits Compared to Real-Time Reverse Transcriptase-Polymerase Chain Reaction (rRT-PCR) Among Clinical Samples

Background and objective The coronavirus disease 2019 (COVID-19) pandemic has imposed a significant burden on healthcare systems worldwide. This highlights the need for simple, rapid, and affordable diagnostic tests that can serve as alternatives to the existing costly and demanding polymerase chain reaction (PCR) assay, especially in resource-limited countries like Ghana. In light of this, we aimed to assess the diagnostic efficacy of three COVID-19 rapid immunochromatographic antigen test kits vs. real-time reverse transcriptase-PCR (rRT-PCR). Methods This study evaluated the sensitivity and specificity of three COVID-19 rapid immunochromatographic antigen test kits: DG Rapid, SD Rapid, and SS Rapid. They were compared with the gold standard RT-PCR for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen in 75 randomly selected archived nasopharyngeal samples. Results Of the 75 samples tested, 38 (50.7%) were positive and 37 (49.3%) were negative for SARS-CoV-2 RNA by rRT-PCR assay. No false positives were recorded. On the other hand, the DG Rapid kit detected 30 (78.9%) true positives and eight (21.1%) false negatives. SD Rapid kit detected 28 (73.7%) true positives and 10 (26.3%) false negatives, while the SS Rapid kit detected 19 (50.0%) true positives and 19 (50.0%) false negatives. While the specificity of each test kit was 100% (95% CI), the sensitivity of the DG Rapid, SD Rapid, and SS Rapid kits was 79%, 74%, and 50% (95% CI), respectively. Higher sensitivities were recorded among samples with cycle threshold (Ct) values <29.99 for each kit. Also, the DG Rapid kit demonstrated 79% excellent agreement with rRT-PCR, while the SD Rapid and SS Rapid kits demonstrated good agreement with rRT-PCR with 73% and 50% Cohen's kappa values, respectively. Conclusions Based on our findings, DG Rapid and SD Rapid kits are reliable alternatives to rRT-PCR for the detection of SARS-CoV-2 infection, especially in resource-limited settings like Ghana.

COVID-19 response in a long-term care facility for people with epilepsy

OBJECTIVE

To assess asymptomatic rates and severity of SARS-CoV-2 infection in people with epilepsy and their healthcare workers in a long-term care facility which had implemented weekly surveillance testing between April 2020 and June 2022.

METHODS

Questionnaires focused on objective and subjective COVID-19 symptoms for people with epilepsy residing in and their healthcare workers at the Chalfont Centre for Epilepsy in June 2022. Demographic information, comorbidities, and seizure frequency were gathered from medical records. We also collected responses on objective and subjective COVID-19 symptoms from healthcare workers who participated in a prospective study assessing the reaction to COVID-19 vaccinations (SAFER).

RESULTS

Fifty-five out of 89 (62%) residents tested positive at least once on weekly PCR testing for SARS-CoV-2 during the period of interest; 20 of those (37%) were asymptomatic. In comparison, of those 63 healthcare workers who tested positive at least once on weekly testing during the same period, only four (6%) were asymptomatic. Of the 159 healthcare workers who also participated in the SAFER study, 41 tested positive at least once, and seven (17%) were completely asymptomatic during infection with SARS-CoV-2.

SIGNIFICANCE

People with epilepsy living in a long-term care facility were more likely to present with asymptomatic SARS-CoV-2 infections than healthcare workers at the same facility. Despite possible bias in the reporting of subjective symptoms due to management-by-proxy, there is no evidence that vulnerable people living in an epilepsy long-term care facility showed reduced resilience towards infections.

PLAIN LANGUAGE SUMMARY

People with epilepsy living in care home facilities had a surprisingly high degree of asymptomatic infections with SARS-CoV-2. Very few residents had severe or fatal outcomes. This is in stark contrast to the widely reported bad outcomes for people without epilepsy in other care homes. People with epilepsy reported significantly less symptoms than their healthcare workers. No changes in seizure frequency during or after infection were observed.

Retrospective estimation of the time-varying effective reproduction number for a COVID-19 outbreak in Shenyang, China: An observational study

The time-varying effective reproduction number Re(t) is essential for designing and adjusting public health responses. Retrospective analysis of Re(t) helps to evaluate health emergency capabilities. We conducted this study to estimate the Re(t) of the Corona Virus Disease 2019 (COVID-19) outbreak caused by SARS-CoV-2 Omicron in Shenyang, China. Data on the daily incidence of this Corona Virus Disease 2019 outbreak between March 5, 2022, and April 25, 2022, in Shenyang, China, were downloaded from the Nationwide Notifiable Infectious Diseases Reporting Information System. Infector-infectee pairs were identified through epidemiological investigation. Re(t) was estimated by R-studio Package "EpiEstim" based on Bayesian framework through parameter and nonparametric method, respectively. About 1134 infections were found in this outbreak, with 20 confirmed cases and 1124 asymptomatic infections. Fifty-four infector-infectee pairs were identified and formed a serial interval list, and 15 infector-infectee pairs were included in the generation time table. Re(t) calculated by parameter and nonparametric method all peaked on March 17, 2022, with a value of 2.58 and 2.54 and decreased to <1 after March 28, 2022. There was no statistical difference in the Re(t) distribution calculated using the 2 methods (t = 0.001, P > .05). The present study indicated that the decisive response of Shenyang, China, played a significant role in preventing the spread of the epidemic, and the retrospective analysis provided novel insights into the outbreak response to future public health emergencies.

ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses

Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.

A closer look at the link between cycle threshold, clinical features and biomarkers: An observational study in COVID-19 patients

Background

Symptoms for severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) appear 2-3 days after exposure to the virus. Being a virus, detection is primarily by polymerase chain reaction as this offers superior sensitivity and specificity. There was a misconception that patients with low cycle threshold (Ct) have severe coronavirus disease (COVID), and for individuals with higher Ct, it is the other way around. The prognosis for COVID was derived from various biomarkers and physicians heavily relied on them.

Materials and Methods

A cross-sectional study spanning a duration of 2 years was conducted at a tertiary care centre in western India. A total of 201 individuals were included and the correlation between Ct, clinical features and biomarkers was studied.

Results

In the E-gene, 43.28% had lower Ct values and 40.79% had low Ct values in the RdRp gene. 50% of all patients had diabetes, with 60% being between the ages of 61 and 80. 54.1% of hypertension patients belonged to ages between 61 and 80. 90.54% of COVID-positive individuals had lactose dehydrogenase levels ranging from 440 to 760. 79% of patients had a procalcitonin value of more than one but less than six. 79.1% of patients had an erythrocyte sedimentation rate between 36 and 90.

Conclusion

Ct value though has a research value; it is a poor prognostic marker when compared to the various biomarkers that have been studied earlier. We cannot conclusively state that all our findings are accurate due to a lack of data but further research into the prognostic value of Ct should be conducted which will help in the ongoing scenario.

COVID-19 outbreak and genomic investigation in an inpatient behavioral health unit

Background

Inpatient behavioral health units (BHUs) had unique challenges in implementing interventions to mitigate coronavirus disease 2019 (COVID-19) transmission, in part due to socialization in BHU settings. The objective of this study was to identify the transmission routes and the efficacy of the mitigation strategies employed during a COVID-19 outbreak in an inpatient BHU during the Omicron surge from December 2021 to January 2022.

Methods

An outbreak investigation was performed after identifying 2 COVID-19-positive BHU inpatients on December 16 and 20, 2021. Mitigation measures involved weekly point prevalence testing for all inpatients, healthcare workers (HCWs), and staff, followed by infection prevention mitigation measures and molecular surveillance. Whole-genome sequencing on a subset of COVID-19-positive individuals was performed to identify the outbreak source. Finally, an outbreak control sustainability plan was formulated for future BHU outbreak resurgences.

Results

We identified 35 HCWs and 8 inpatients who tested positive in the BHU between December 16, 2021, and January 17, 2022. We generated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomes from 15 HCWs and all inpatients. Phylogenetic analyses revealed 3 distinct but genetically related clusters: (1) an HCW and inpatient outbreak likely initiated by staff, (2) an HCW and inpatient outbreak likely initiated by an inpatient visitor, and (3) an HCW-only cluster initiated by staff.

Conclusions

Distinct transmission clusters are consistent with multiple, independent SARS-CoV-2 introductions with further inpatient transmission occurring in communal settings. The implemented outbreak control plan comprised of enhanced personal protective equipment requirements, limited socialization, and molecular surveillance likely minimized disruptions to patient care as a model for future pandemics.

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study

Background

Understanding routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in long-term care facilities is essential for the development of effective control measures.

Methods

Between March 1, 2020, and August 31, 2023, we identified coronavirus disease 2019 (COVID-19) cases among residents and employees in a Veterans Affairs community living center that conducted routine screening for asymptomatic COVID-19. Contact tracing was conducted to identify suspected transmission events, and whole genome sequencing was performed to determine the relatedness of SARS-CoV-2 samples.

Results

During the 42-month study period, 269 cases of COVID-19 were diagnosed, including 199 employees and 70 residents. A total of 48 (24.1%) employees and 30 (42.9%) residents were asymptomatic. Sequencing analysis provided support for multiple events in which employees transmitted SARS-CoV-2 to co-workers and residents. There was 1 episode of likely transmission of SARS-CoV-2 from one resident to another resident, but no documented transmissions from residents to employees.

Conclusions

Transmission of SARS-CoV-2 in the community living center predominantly involved transmission from employees to co-workers and residents. There is a need for improved measures to prevent transmission of SARS-CoV-2 by healthcare personnel.

Commensal bacteria inhibit viral infections via a tryptophan metabolite

There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance to infection. We experimentally validated these findings by demonstrating two different Lachnospiraceae isolates, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo. Given the link between tryptophan catabolism and HIV disease severity, we found that an isogenic mutant of C. immunis that lacks the aromatic amino acid aminotransferase (ArAT) gene, which is key to metabolizing tryptophan into 3-indolelactic acid (ILA), no longer inhibits HIV infection. Intriguingly, we confirmed that a second commensal bacterium also inhibited HIV in an ArAT-dependent manner, thus establishing the generalizability of this finding. In addition, we found that purified ILA inhibited HIV infection by agonizing the aryl hydrocarbon receptor (AhR). Given that the AhR has been implicated in the control of multiple viral infections, we demonstrated that C. immunis also inhibited human cytomegalovirus (HCMV) infection in an ArAT-dependent manner. Importantly, metagenomic analysis of individuals at-risk for HIV revealed that those who ultimately acquired HIV had a lower fecal abundance of the bacterial ArAT gene compared to individuals who did not, which indicates our findings translate to humans. Taken together, our results provide mechanistic insights into how commensal bacteria decrease susceptibility to viral infections. Moreover, we have defined a microbiota-driven antiviral pathway that offers the potential for novel therapeutic strategies targeting a broad spectrum of viral pathogens.

Magnitude and determinants of excess total, age-specific and sex-specific all-cause mortality in 24 countries worldwide during 2020 and 2021: results on the impact of the COVID-19 pandemic from the C-MOR project

INTRODUCTION

To examine the impact of the COVID-19 pandemic on mortality, we estimated excess all-cause mortality in 24 countries for 2020 and 2021, overall and stratified by sex and age.

METHODS

Total, age-specific and sex-specific weekly all-cause mortality was collected for 2015-2021 and excess mortality for 2020 and 2021 was calculated by comparing weekly 2020 and 2021 age-standardised mortality rates against expected mortality, estimated based on historical data (2015-2019), accounting for seasonality, and long-term and short-term trends. Age-specific weekly excess mortality was similarly calculated using crude mortality rates. The association of country and pandemic-related variables with excess mortality was investigated using simple and multilevel regression models.

RESULTS

Excess cumulative mortality for both 2020 and 2021 was found in Austria, Brazil, Belgium, Cyprus, England and Wales, Estonia, France, Georgia, Greece, Israel, Italy, Kazakhstan, Mauritius, Northern Ireland, Norway, Peru, Poland, Slovenia, Spain, Sweden, Ukraine, and the USA. Australia and Denmark experienced excess mortality only in 2021. Mauritius demonstrated a statistically significant decrease in all-cause mortality during both years. Weekly incidence of COVID-19 was significantly positively associated with excess mortality for both years, but the positive association was attenuated in 2021 as percentage of the population fully vaccinated increased. Stringency index of control measures was positively and negatively associated with excess mortality in 2020 and 2021, respectively.

CONCLUSION

This study provides evidence of substantial excess mortality in most countries investigated during the first 2 years of the pandemic and suggests that COVID-19 incidence, stringency of control measures and vaccination rates interacted in determining the magnitude of excess mortality.

A joint Bayesian hierarchical model for estimating SARS-CoV-2 genomic and subgenomic RNA viral dynamics and seroconversion

Understanding the viral dynamics of and natural immunity to the severe acute respiratory syndrome coronavirus 2 is crucial for devising better therapeutic and prevention strategies for coronavirus disease 2019 (COVID-19). Here, we present a Bayesian hierarchical model that jointly estimates the genomic RNA viral load, the subgenomic RNA (sgRNA) viral load (correlated to active viral replication), and the rate and timing of seroconversion (correlated to presence of antibodies). Our proposed method accounts for the dynamical relationship and correlation structure between the two types of viral load, allows for borrowing of information between viral load and antibody data, and identifies potential correlates of viral load characteristics and propensity for seroconversion. We demonstrate the features of the joint model through application to the COVID-19 post-exposure prophylaxis study and conduct a cross-validation exercise to illustrate the model's ability to impute the sgRNA viral trajectories for people who only had genomic RNA viral load data.

Single-center Outcomes After Liver Transplantation With SARS-CoV-2-Positive Donors: An Argument for Increased Utilization

Background

The COVID-19 pandemic has led to an increase in SARS-CoV-2-test positive potential organ donors. The benefits of life-saving liver transplantation (LT) must be balanced against the potential risk of donor-derived viral transmission. Although emerging evidence suggests that the use of COVID-19-positive donor organs may be safe, granular series thoroughly evaluating safety are still needed. Results of 29 consecutive LTs from COVID-19-positive donors at a single center are presented here.

Methods

A retrospective cohort study of LT recipients between April 2020 and December 2022 was conducted. Differences between recipients of COVID-19-positive (n = 29 total; 25 index, 4 redo) and COVID-19-negative (n = 472 total; 454 index, 18 redo) deceased donor liver grafts were compared.

Results

COVID-19-positive donors were significantly younger (P = 0.04) and had lower kidney donor profile indices (P = 0.04) than COVID-19-negative donors. Recipients of COVID-19-positive donor grafts were older (P = 0.04) but otherwise similar to recipients of negative donors. Donor SARS-CoV-2 infection status was not associated with a overall survival of recipients (hazard ratio, 1.11; 95% confidence interval, 0.24-5.04; P = 0.89). There were 3 deaths among recipients of liver grafts from COVID-19-positive donors. No death seemed virally mediated because there was no qualitative association with peri-LT antispike antibody titers, post-LT prophylaxis, or SARS-CoV-2 variants.

Conclusions

The utilization of liver grafts from COVID-19-positive donors was not associated with a decreased overall survival of recipients. There was no suggestion of viral transmission from donor to recipient. The results from this large single-center study suggest that COVID-19-positive donors may be used safely to expand the deceased donor pool.

Progranulin promotes regulatory T cells plasticity by mitochondrial metabolism through AMPK/PGC-1α pathway in ARDS

As the aging population increases, the focus on elderly patients with acute respiratory distress syndrome (ARDS) is also increasing. In this article, we found progranulin (PGRN) differential expression in ARDS patients and healthy controls, even in young and old ARDS patients. Its expression strongly correlates with several cytokines in both young and elderly ARDS patients. PGRN has comparable therapeutic effects in young and elderly mice with lipopolysaccharide-induced acute lung injury, manifesting as lung injury, apoptosis, inflammation, and regulatory T cells (Tregs) differentiation. Considering that Tregs differentiation relies on metabolic reprogramming, we discovered that Tregs differentiation was mediated by mitochondrial function, especially in the aged population. Furthermore, we demonstrated that PGRN alleviated the mitochondrial damage during Tregs differentiation through the AMPK/PGC-1α pathway in T cells. Collectively, PGRN may regulate mitochondria function to promote Tregs differentiation through the AMPK/PGC-1α pathway to improve ARDS.

Molecular Epidemiology of SARS-CoV-2 within Accra Metropolis Postlockdown

Introduction

Currently, sequencing has been the only tool for the identification of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants. However, it is known to be an expensive and laborious approach involving high technical expertise. Considering the reduced adherence to preventive measures postlockdown in Accra, this study presents an alternative method that leverages polymerase chain reaction (PCR) to identify circulating SARS-CoV-2 variants in the Accra Metropolis postlockdown.

Methods

This prospective cross-sectional study was conducted between July and December 2022. Nasopharyngeal samples were collected from 268 consenting participants. Samples were subjected to nucleic acid extraction and followed by real-time polymerase chain reaction for the detection and quantification of SARS-CoV-2 RNA. SARS-CoV-2 positive samples were subsequently subjected to variant identification using rapid PCR. Findings. The prevalence of SARS-CoV-2 within the Accra Metropolis was 30.2%. The majority of the SARS-CoV-2 infection was diagnosed in females, participants aged 41-50 years, and symptomatic participants. Participants aged ≤10 years and females recorded the highest viral load while participants aged 41-50 years recorded the highest number of infections. The SARS-CoV-2 variants detected were Alpha (64.2%), Delta (22.2%), and Omicron (13.6%). Predictors of SARS-CoV-2 infection identified were chills, cough, headache, body weakness, sore throat, and dyspnoea in order of decreasing association with SARS-CoV-2 infection. There was a strong association between symptom status, gender, age, and SARS-CoV-2 infection.

Conclusion

There was a high prevalence of SARS-CoV-2 within the Accra Metropolis postlockdown within the sampling period. The Alpha variant of SARS-CoV-2 is the predominant circulating variant, and persons presenting with symptoms are most likely to be diagnosed with COVID-19. Children aged ≤10 years serve as a reservoir for infection transmission.

Timing and Predictors of Loss of Infectivity Among Healthcare Workers With Mild Primary and Recurrent COVID-19: A Prospective Observational Cohort Study

BACKGROUND

There is a need to understand the duration of infectivity of primary and recurrent coronavirus disease 2019 (COVID-19) and identify predictors of loss of infectivity.

METHODS

Prospective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US Centers for Disease Control and Prevention (CDC) criteria (fever resolution, symptom improvement, and negative RADT) to predict loss of infectivity was also investigated.

RESULTS

In total, 121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n = 107, 88.4%) had received ≥3 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 odds ratio [OR], 0.14; P < .001]; day 7 OR, 0.04; P = .003]) and were all non-infective by day 10 (P = .02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; P = .003), an RT-PCR cycle threshold [Ct] value <23 (aOR on day 5, 22.75; P < .001) but not symptom improvement or RADT result.The CDC criteria would identify 36% (24/67) of all non-infectious individuals on day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture.

CONCLUSIONS

Infectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.

Control of SARS-CoV-2 infection in skilled nursing facilities in Detroit, Michigan: a model for emerging infectious diseases

An infection prevention bundle that consisted of the development of a response team, public-academic partnership, daily assessment, regular testing, isolation, and environmental controls was implemented in 26 skilled nursing facilities in Detroit, Michigan (March 2020-April 2021). This intervention was associated with sustained control of severe acute respiratory coronavirus virus 2 infection among residents and staff.

Early predictors of intensive care unit admission among COVID-19 patients in Qatar

Background

COVID-19 is associated with significant morbidity and mortality. This study aimed to explore the early predictors of intensive care unit (ICU) admission among patients with COVID-19.

Methods

This was a case-control study of adult patients with confirmed COVID-19. Cases were defined as patients admitted to ICU during the period February 29-May 29, 2020. For each case enrolled, one control was matched by age and gender.

Results

A total of 1,560 patients with confirmed COVID-19 were included. Each group included 780 patients with a predominant male gender (89.7%) and a median age of 49 years (interquartile range = 18). Predictors independently associated with ICU admission were cardiovascular disease (adjusted odds ratio (aOR) = 1.64, 95% confidence interval (CI): 1.16-2.32, p = 0.005), diabetes (aOR = 1.52, 95% CI: 1.08-2.13, p = 0.016), obesity (aOR = 1.46, 95% CI: 1.03-2.08, p = 0.034), lymphopenia (aOR = 2.69, 95% CI: 1.80-4.02, p < 0.001), high AST (aOR = 2.59, 95% CI: 1.53-4.36, p < 0.001), high ferritin (aOR = 1.96, 95% CI: 1.40-2.74, p < 0.001), high CRP (aOR = 4.09, 95% CI: 2.81-5.96, p < 0.001), and dyspnea (aOR = 2.50, 95% CI: 1.77-3.54, p < 0.001).

Conclusion

Having cardiovascular disease, diabetes, obesity, lymphopenia, dyspnea, and increased AST, ferritin, and CRP were independent predictors for ICU admission in patients with COVID-19.

Latent and incubation periods of Delta, BA.1, and BA.2 variant cases and associated factors: a cross-sectional study in China

BACKGROUND

The latent and incubation periods characterize the transmission of infectious viruses and are the basis for the development of outbreak prevention and control strategies. However, systematic studies on the latent period and associated factors with the incubation period for SAS-CoV-2 variants are still lacking. We inferred the two durations of Delta, BA.1, and BA.2 cases and analyzed the associated factors.

METHODS

The Delta, BA.1, and BA.2 (and its lineages BA.2.2 and BA.2.76) cases with clear transmission chains and infectors from 10 local SAS-CoV-2 epidemics in China were enrolled. The latent and incubation periods were fitted by the Gamma distribution, and associated factors were analyzed using the accelerated failure time model.

RESULTS

The mean latent period for 672 Delta, 208 BA.1, and 677 BA.2 cases was 4.40 (95%CI: 4.24 ~ 4.63), 2.50 (95%CI: 2.27 ~ 2.76), and 2.58 (95%CI: 2.48 ~ 2.69) days, respectively, with 85.65% (95%CI: 83.40 ~ 87.77%), 97.80% (95%CI: 96.35 ~ 98.89%), and 98.87% (95%CI: 98.40 ~ 99.27%) of them starting to shed viruses within 7 days after exposure. In 405 Delta, 75 BA.1, and 345 BA.2 symptomatic cases, the mean latent period was 0.76, 1.07, and 0.79 days shorter than the mean incubation period [5.04 (95%CI: 4.83 ~ 5.33), 3.42 (95%CI: 3.00 ~ 3.89), and 3.39 (95%CI: 3.24 ~ 3.55) days], respectively. No significant difference was observed in the two durations between BA.1 and BA.2 cases. After controlling for the sex, clinical severity, vaccination history, number of infectors, the length of exposure window and shedding window, the latent period [Delta: exp(β) = 0.81, 95%CI: 0.66 ~ 0.98, p = 0.034; Omicron: exp(β) = 0.82, 95%CI: 0.71 ~ 0.94, p = 0.004] and incubation period [Delta: exp(β) = 0.69, 95%CI: 0.55 ~ 0.86, p < 0.001; Omicron: exp(β) = 0.83, 95%CI: 0.72 ~ 0.96, p = 0.013] were significantly shorter in 18 ~ 49 years but did not change significantly in ≥ 50 years compared with 0 ~ 17 years.

CONCLUSION

Pre-symptomatic transmission can occur in Delta, BA.1, and BA.2 cases. The latent and incubation periods between BA.1 and BA.2 were similar but shorter compared with Delta. Age may be associated with the latent and incubation periods of SARS-CoV-2.

Bio-based ionic liquid filter with enhanced electrostatic attraction for outside filtration and inside collection of viral aerosols

Hazardous biological pathogens in the air pose a significant public environmental health concern as infected individuals emit virus-laden aerosols (VLAs) during routine respiratory activities. Mask-wearing is a key preventive measure, but conventional filtration methods face challenges, particularly in high humidity conditions, where electrostatic charge decline increases the risk of infection. This study introduces a bio-based air filter comprising glycine ionic liquids (GILs) and malleable polymer composite (GILP) with high polarity and functional group density, which are wrapped around a melamine-formaldehyde (MF) resin skeleton, forming a conductive, porous GIL functionized ionic network air filter (GILP@MF). When subjected to low voltage, the GILP@MF composite efficiently captures VLAs including nanoscale virus particles through the enhanced electrostatic attraction, especially in facing high humidity bioaerosols exhaled by human body. The filtration/collection efficiency and quality factor can reach 98.3% and 0.264 Pa-1 at 0.1 m s-1, respectively. This innovative filter provides effective VLA protection and offers potential for non-invasive respiratory virus sampling, advancing medical diagnosis efforts.