Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020

Up-to-date nucleic acid assays for diagnosing respiratory infection

Nucleic acid assays have been widely used as rapid tests for diagnosing respiratory infections during and after the coronavirus disease 2019 (COVID-19) pandemic. An ideal point-of-care diagnostic must be affordable, sensitive, specific, user-friendly, rapid/robust, equipment-free and deliverable (ASSURED), and in addition to improvements to conventional methods based on polymerase chain reaction (PCR), point-of-care testing aiming for "REASSURED" are emerging through integration with microfluidic technology. Compared to conventional immunoassays, nucleic acid assays, especially rapid nucleic acid assays as point-of-care testing, contribute to improvements in various clinical outcomes, such as diagnostic yield, turnaround time, length of hospital stay, disease treatment, and infection control management. Rapid and diverse development of new nucleic acid-based molecular diagnostic technologies, such as those based on the CRISPR/Cas system or biosensor nucleic acid assays, is expected to become increasingly diverse in the future as point-of-care testing. In addition, laboratory-based DNA sequencing technology has been used to perform microbiome analyses over a wide area and is expected to shed light on the pathological mechanisms of various respiratory infectious diseases. One example of the benefits of nucleic acid amplification analysis methods is their ability to reveal the true nature of the bacterial flora in pneumonia lesions. This has been demonstrated based on the results of 16S ribosomal RNA gene sequencing analyses using bronchoalveolar lavage fluid directly obtained from pneumonia lesions in patients with pneumonia.

Hybrid analysis with phylogeny and population modeling to estimate the recent founding date of a population: A case study in the origins of COVID-19 illustrates how a branching process approximation can simplify a hybrid analysis

The exact date of the primary infection in COVID-19 remains unknown. One influential article (Pekar et al. (2021)) estimated the date with a hybrid analysis combining epidemiological and phylogenetic methods. The phylogenetic methods analyzed 583 SARS-COV-2 complete genomes to estimate the sample tMRCA (time of the most recent common ancestor). Before igniting as an epidemic, however, COVID-19 may have had several population bottlenecks with only a single infected person, so the MRCA merely represents the last such bottleneck. Pekar et al. (2021) therefore used epidemiological methods to estimate the time from the primary infection to the sample MRCA. The hybrid method involved several arbitrary decisions, however, reflecting the fact that the epidemiological and phylogenetic analyses overlap at the sample MRCA and are generally probabilistically dependent. Towards removing the dependence, note that the start of an epidemic has a branching process approximation. Let the branching process have a single ancestor. If the branching process does not go extinct, define skeleton particles (individuals) to be particles whose lineages do not go extinct, and define the long-time MRCA as the earliest skeleton particle with at least two skeleton offspring. A linear phylogeny of skeleton particles therefore separates the ancestor from the long-time MRCA. Probabilistically, the linear phylogeny is a defective renewal process of skeleton particles, making the generation count geometrically distributed. Moreover, the terminology "long-time MRCA" is apt, because as time becomes arbitrarily large, the MRCA of the corresponding extant population approaches the long-time MRCA. Effectively, the focus on the long-time MRCA makes the forward epidemiological and backward phylogenetic analyses probabilistically independent. The present article can therefore confirm most of the epidemiological conclusions of the hybrid analysis of Pekar et al. (2021). Its use of branching process approximations also points the way to noticeable simplifications in the hybrid method.

A comprehensive validation study on the influencing factors of cough-based COVID-19 detection through multi-center data with abundant metadata

OBJECTIVE

In recent years, COVID-19 has placed enormous burdens on healthcare systems. Currently, hundreds of thousands of new cases are reported monthly. World Health Organization is managing COVID-19 as a long-term disease, indicating that an efficient and low-cost detection method remains necessary. Previous studies have shown competitive results on cough-based COVID-19 detection combined with deep learning methods. However, most studies have focused only on improving classification performance on single-source data while neglecting the impact of various factors in real-world applications.

METHODS

To this end, we collected clinical and large-scale crowdsourced cough audios with abundant metadata to comprehensively validate the performance differences among different groups. Specifically, we leveraged self-supervised learning for pre-training and fine-tuned the model with data from different sources. Then based on the metadata, we compared the effects of factors such as cough types, symptoms, and infection stages on detection performance. Moreover, we recorded clinical indicators of viral load and antibody levels and observed the correlation between predicted probabilities and indicator values for the first time. Several open-source datasets were tested to verify the model generalizability.

RESULTS

The area under receiver operating characteristic curve is 0.79 for clinical data and 0.69 for crowdsourced data, indicating differences between clinical validation and real-world application. The performance in detecting symptomatic COVID-19 subjects is usually better than detecting asymptomatic COVID-19 subjects. The prediction results show weak correlation with clinical indicators on a small number of clinical data. Poor detection performance in recovery individuals and open-source datasets shows a limitation of existing cough-based detection models.

CONCLUSION

Our study validated the model performance and limitations using multi-source data with abundant metadata, which helped researchers evaluate the feasibility of cough-based COVID-19 detection model in practical applications.

Estimating the effect of COVID-19 vaccination and prior infection on cycle threshold values as a proxy of SARS-CoV-2 viral load

OBJECTIVES

SARS-CoV-2 viral load could be an important parameter for transmission potential. Here, we use quantitative reverse transcription-polymerase chain reaction cycle threshold (Ct) values as a proxy for viral load. We assess the effect of COVID-19 vaccination and prior infection status on Ct value while accounting for the virus variant.

METHODS

Using Dutch SARS-CoV-2 community testing data (n = 409,925 samples) from 8 March 2021 to 31 December 2022, separate univariable linear regressions were conducted for each explanatory variable, including age, sex, testing date, variant of infection, time since symptom onset, and testing laboratory. Subsequently, causal inference analysis assessed the impact of prior infection and vaccination status on Ct values, employing inverse propensity score weighting to adjust for confounders.

RESULTS

Our findings revealed a negative correlation between age and Ct values. Additionally, we observed modest differences in Ct values between different variants of infection, with lower Ct values (indicative of higher viral load) noted for Omicron variants compared to earlier variants. In addition, our results indicated an increase in Ct value (lower viral load) with prior infection. Conversely, the impact of vaccination was less pronounced.

CONCLUSIONS

We observed an association between prior infection status and higher Ct values, suggesting a decrease in viral load, which could possibly indicate lower transmissibility.

Investigating the relationship between cycle threshold of SARS-CoV-2 RT-PCR, clinical features, and laboratory data in hospitalized COVID-19 patients in Semnan, Iran

Introduction

COVID-19, caused by the SARS-CoV-2 virus, has emerged as a global public health crisis. Understanding the factors associated with disease severity and outcomes is crucial for effective patient management. This study aimed to investigate the association between cycle threshold (CT) values, demographic data, medical history, clinical manifestations, and laboratory findings in hospitalized COVID-19 patients in Semnan, Iran.

Methods

A cross-sectional study was conducted on 86 patients with confirmed COVID-19 admitted to two hospitals in Semnan, Iran, between December 2022 and March 2023. Respiratory swab samples were collected RT-PCR was performed, CT values were obtained, and data were collected from medical records, including demographic information, medical history, clinical manifestations, and laboratory results. Statistical analysis was performed using SPSS software.

Results

The study included 86 COVID-19 patients, with a slightly higher representation of females (55.8%) and a mean age of 67.43 years. Pre-existing conditions like hypertension, diabetes mellitus, and ischemic heart disease were prevalent among hospitalized patients. A majority of patients (59.3%) had severe COVID-19, as indicated by lower CT values, while 31.4% exhibited oxygen saturation levels below 90%. Significant differences were observed in FBS, CRP, WBC, Hb, Cr, and SPo2 levels between severe and non-severe patients. Correlation analysis revealed associations between age, CRP, Cr, BUN, FBS, Vitamin D, TG, LDL, HDL, AST, ALP, and SPo2. Reflecting complex interactions between inflammatory markers, organ function, and lipid metabolism in COVID-19 patients.

Conclusion

This study provides valuable insights into the association between CT values, clinical characteristics, and laboratory findings in hospitalized COVID-19 patients. The findings underscore the importance of CT values in assessing disease severity and potential prognostication. Further research is warranted to validate these findings in larger and more diverse patient populations.

Intersecting SARS-CoV-2 spike mutations and global vaccine efficacy against COVID-19

In line with encountering the world with the emergence of vaccine-resistance variants of SARS-CoV-2, 15,669,529 samples that received COVID-19 vaccines until April 2023 were investigated as two doses in the first phase and booster vaccinations in the second phase. The analysis shows that D614G and P681 mutations occurred in both phases. The E484 and Y655 mutations significantly emerged during the second phase. The 762-889 and 254-381 regions are revealed as conserved parts and could be considered in vaccine design. The Kruskal-Wallis test revealed a significant reduction in single mutations between populations with 20%-50% and those with 70%-100% vaccination coverage (p=0.017). The Mann-Whitney U test proposes a link between vaccination and suppression of viral mutation rates. Dynamic modeling suggests that key mutations have facilitated the virus' evolution and immune escape. The study's findings are crucial for understanding virus genome mutations, especially E614 and P681 in Delta and E484 and H655 in Omicron. This highlights the need to adjust strategies and strengthen global efforts in combating the pandemic.

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.

Predictability of viral load dynamics in the early phases of SARS-CoV-2 through a model-based approach

A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide robust predictions of the epidemic dynamics. We focused on viral load kinetics whose dynamical features are typically available in the symptomatic stage of the infection. Hence, the epidemiological evolution was obtained by relying on a compartmental approach characterized by a varying infection rate to estimate early-stage viral load dynamics, of which few data are available. We tested the proposed approach with real data of SARS-CoV-2 viral load kinetics collected from patients living in an Italian province. The considered database refers to early-phase infections, whose viral load kinetics have not been affected by the mass vaccination policies in Italy.

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.

Interpretation of indoor air surveillance for respiratory infections: a prospective longitudinal observational study in a childcare setting

BACKGROUND

Sampling the air in indoor congregate settings, where respiratory pathogens are ubiquitous, may constitute a valuable yet underutilised data source for community-wide surveillance of respiratory infections. However, there is a lack of research comparing air sampling and individual sampling of attendees. Therefore, it remains unclear how air sampling results should be interpreted for the purpose of surveillance.

METHODS

In this prospective observational study, we compared the presence and concentration of several respiratory pathogens in the air with the number of attendees with infections and the pathogen load in their nasal mucus. Weekly for 22 consecutive weeks, we sampled the air in a single childcare setting in Belgium. Concurrently, we collected the paper tissues used to wipe the noses of 23 regular attendees: children aged zero to three and childcare workers. All samples were tested for 29 respiratory pathogens using PCR.

FINDINGS

Air sampling sensitively detected most respiratory pathogens found in nasal mucus. Some pathogens (SARS-CoV-2, Pneumocystis jirovecii) were found repeatedly in the air, but rarely in nasal mucus, whilst the opposite was true for others (Human coronavirus NL63). All three pathogens with a clear outbreak pattern (Human coronavirus HKU-1, human parainfluenza virus 3 and 4) were found in the air one week before or concurrent with the first detection in paper tissue samples. The presence and concentration of pathogens in the air was best predicted by the pathogen load of the most infectious case. However, air pathogen concentrations also correlated with the number of attendees with infections. Detection and concentration in the air were associated with CO2 concentration, a marker of ventilation and occupancy.

INTERPRETATION

Our results suggest that air sampling could provide sensitive, responsive epidemiological indicators for the surveillance of respiratory pathogens. Using air CO2 concentrations to normalise such signals emerges as a promising approach.

FUNDING

KU Leuven; DURABLE project, under the EU4Health Programme of the European Commission; Thermo Fisher Scientific.

Inferring transmission risk of respiratory viral infection from the viral load kinetics of SARS-CoV-2, England, 2020 to 2021 and influenza A virus, Hong Kong, 2008 to 2012

BackgroundInfectiousness of respiratory viral infections is quantified as plaque forming units (PFU), requiring resource-intensive viral culture that is not routinely performed. We hypothesised that RNA viral load (VL) decline time (e-folding time) in people might serve as an alternative marker of infectiousness.AimThis study's objective was to evaluate the association of RNA VL decline time with RNA and PFU VL area under the curve (AUC) and transmission risk for SARS-CoV-2 and influenza A virus.MethodsIn SARS-CoV-2 and influenza A virus community cohorts, viral RNA was quantified by reverse transcription quantitative PCR in serial upper respiratory tract (URT)-samples collected within households after an initial household-member tested positive for one virus. We evaluated correlations between RNA VL decline time and RNA and PFU-VL AUC. Associations between VL decline time and transmission risk in index-contact pairs were assessed.ResultsIn SARS-CoV-2 cases, we observed positive correlations between RNA VL decline time and RNA and PFU VL AUC with posterior probabilities 1 and 0.96 respectively. In influenza A cases a positive correlation between RNA VL decline time and RNA VL AUC was observed, with posterior probability of 0.87. Index case VL decline times one standard deviation above the cohort-mean showed a relative increase in secondary attack rates of 39% (95% credible interval (CrI): -6.9 to 95%) for SARS-CoV-2 and 25% (95% CrI: -11 to 71%) for influenza A virus.ConclusionWe identify VL decline time as a potential marker of infectiousness and transmission risk for SARS-CoV-2 and influenza A virus. Early ascertainment of VL kinetics as part of surveillance of new viruses or variants could inform public health decision making.

Influence of easing COVID-19 strategies following downgrading of the national infectious disease category on COVID-19 occurrence among hospitalized patients in Japan

PURPOSE

We aimed to evaluate the influence of easing COVID-19 preventive measures following its downgrading to a common infectious disease on COVID-19 occurrence among hospitalized patients.

METHODS

Nosocomial occurrence of COVID-19 was compared between periods with national infectious disease category 5 versus the preceding category 2 equivalent. Changes in the revised manual included a shorter duration of work restrictions for infected health care practitioners (HCPs); no work restriction for HCPs exposed to SARS-CoV-2 with a negative test on days 1, 3 and 5; discontinuation of universal pre-admission screening; and pre-emptive isolation of patients without screening. Wearing an N95 mask and face shield was required in procedure/care with moderate-to high-risk contact.

RESULTS

Although the mean monthly number of infected HCPs increased from 8.1 to 12.7 in the category 5 period (p = 0.034) and that of pre-admission screening decreased to one-fourth, the COVID-19 incidence in hospitalized patients remained similar between the two study periods (1.60 ± 5.59/month versus 1.40 ± 2.63/month, p = 0.358). Clusters, defined as ≥3 COVID-19 patients on the ward, were experienced twice in the preceding period and only once in the category 5 period. The index cases causing nosocomial SARS-CoV-2 transmission mostly involved rehabilitation therapists in the preceding period; five of six index cases were patients in the category 5 period. Following the expanded indication for N95 masks, neither SARS-CoV-2 transmission to patients nor transmission from infected patients was observed in HCPs for 1 year.

CONCLUSION

With sustained, enhanced standard precautions, easing prevention strategies could limit nosocomial SARS-CoV-2 infections.

Facilitating self-testing with a fast, accurate, and simplified shelf-stable colorimetric LAMP system for Mpox and SARS-CoV-2 detection

The rapid and accurate detection of viral infections is essential for effective disease management and prevention. Quantitative polymerase chain reaction (qPCR) remains the gold standard for viral detection due to its high sensitivity and specificity. However, its limitations-including the need for specialized equipment, trained personnel, and longer processing times-make it impractical for at-home or rapid testing. Although numerous point-of-care assays based on isothermal nucleic acid amplification have been developed, they often lack the simplicity and adaptability required for self-testing in non-laboratory settings such as at home. To address this, we developed and validated the SCOLAR (Shelf-stable Colorimetric LAMP system for Rapid self-testing of viruses) system, a simplified, portable, and accurate diagnostic tool designed for self-testing of Mpox and SARS-CoV-2 infections. The SCOLAR system employs novel lyophilized colorimetric loop-mediated isothermal amplification (LAMP) beads, a customized sample lysis buffer, and smartphone-assisted RGB color analysis for interpreting results. Validation was conducted using 24 mock Mpox skin swabs, 32 wastewater samples, and 104 clinical SARS-CoV-2 nasopharyngeal swabs, with comparisons to an in-house qPCR assay. The SCOLAR system demonstrated an analytical sensitivity of below 10 copies/μL for all targets within 15 min. Diagnostic performance for mock Mpox samples exhibited 93.8 % sensitivity and 100 % specificity, while wastewater samples achieved 100 % sensitivity and specificity. SARS-CoV-2 swabs had 96 % sensitivity and 100 % specificity. The system also proved effective for self-testing by untrained individuals. SCOLAR offers a reliable, easy-to-use platform for rapid self-testing, with potential for broader applications in public health strategies to enhance pandemic preparedness and response.

Environmental biocontamination by SARS-CoV-2 Virus in the hospital setting

Background

Demonstrating the capability to isolate biological material from the environment was fundamental to supporting any transmission route. Various and inconsistent methodologies have been used to address this issue; however, the debate in scientific societies about the possibility of airborne transmission as a source of SARS-CoV-2 spread remained open.

Objective

To analyze SARS-CoV-2 contamination in the air and on surfaces in a hospital setting during the COVID-19 pandemic.

Methods

This study involved air and surface sampling in the emergency, hospitalization, and intensive care unit areas of the Ramón y Cajal University Hospital. A consistent methodology was used for all samples, and clinical and environmental parameters and characterization of each location were recorded.

Results

A total of 234 samples were collected, comprising 160 surface samples and 74 air samples, of which 6.84 % tested positive (13/160 surface samples and 3/74 air samples). High-contact surfaces had the highest proportion of positive samples (12/13). All positive air samples were identified within 2 m of patients who had recently developed symptoms (<5 days). High dependency and elevated temperatures seemed to indicate a higher risk of environmental biocontamination. Additionally, there was a higher risk of contamination in the intensive care units than in the hospitalization or emergency units.

Reagent efficiency and analytical sensitivity optimization for a reliable SARS-CoV-2 pool-based testing strategy

Background

The SARS-CoV-2 pandemic caused millions of infections worldwide. Among the strategies for effective containment, frequent and massive testing was fundamental. Although sample pooling allows multiplying the installed analysis capacity, the definition of the number of samples to include in a pool is commonly guided more by economic parameters than analytical quality.

Methods

We developed a mathematical model to determine the pooling conditions that maximize reagent efficiency and analytical sensitivity. We evaluated 30 samples individually and in 2-sample to 12-sample pools. Using Passing Bablok regressions, we estimated the shift of Ct values in the RT-qPCR reaction for each pool size. With this Ct shift, we estimated sensitivity in the context of the distribution of 1,030 individually evaluated positive samples.

Findings

Our results showed that the most significant gain in efficiency occurred in the 4-sample pool, while at pools greater than 8-sample, there was no considerable reagent savings. Sensitivity significantly dropped to 87.18 %-92.52 % for a 4-sample pool and reached as low as 77.09 %-80.87 % in a 12-sample pooling.

Conclusions

Our results suggest that a 4-sample pooling maximizes reagent efficiency and analytical sensitivity. These considerations are essential to increase testing capacity and efficiently detect and contain contagious.

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.

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.

Epidemiological and Clinical Characteristics of the Course of COVID-19 Among Vaccinated and Unvaccinated Heart Transplant Recipients in Slovenia

Background: Patients receiving heart transplantation require lifelong immunosuppression and compared to the general population, they have a more than five times higher chance of acquiring COVID-19, and their mortality rates are higher. The aim of the present study was to estimate the epidemiological and clinical characteristics of COVID-19 in heart transplant recipients (HTRs) in Slovenia to estimate the vaccination rate and evaluate possible vaccination-hesitant subgroups. Methods: All SARS-CoV-2-positive HTRs (N = 79) between 1 March 2020 and 31 December 2023 at the Infectious Diseases Department, University Medical Centre Ljubljana, Slovenia, were included retrospectively. Demographic, clinical and vaccination data were extracted from medical documentation and a statistical evaluation was performed. Results: The observed vaccination rate was 63.3%, but among patients who received transplants before the pandemic, it was statistically significantly higher (p = 0.027). Vaccinated HTRs were statistically significantly older (p = 0.004) and had a significantly higher Charlson Comorbidity Index (p = 0.018). Our results indicate no significant differences between vaccinated and unvaccinated HTRs regarding acute respiratory insufficiency (p = 0.135), length of hospital stay (p = 0.106), intensive care unit admission (0.414) and in-hospital mortality (p = 0.317), but we observed statistically more frequently an asymptomatic course in those vaccinated (p = 0.050), and a longer length of stay in vector vaccine recipients (p = 0.011) and in those not re-vaccinated (p = 0.030). There was a significantly higher re-vaccination rate in males (p = 0.005). Conclusions: An asymptomatic course of COVID-19 was more often observed in vaccinated HTRs. Our findings suggest statistically significant differences in COVID-19 vaccine acceptance rates; younger HTRs and those transplanted after the pandemic are more hesitant to vaccinate, while females accept booster doses less frequently.

An observational study on imported COVID-19 cases in Hong Kong during mandatory on-arrival hotel quarantine

Background

Hong Kong enforced stringent travel restrictions during the COVID-19 pandemic. Understanding the characteristics of imported COVID-19 cases is important for establishing evidence-based control measures.

Methods

Retrospective cohort study summarising the characteristics of imported cases detected in Hong Kong between 13 November 2020 and 31 January 2022, when compulsory quarantine was implemented.

Findings

A total of 2269 imported COVID-19 cases aged 0-85 years were identified, of which 48.6 % detected on arrival. A shorter median delay from arrival to isolation was observed in Delta and Omicron cases (3 days) than in ancestral strain and other variants cases (12 days; p < 0.001). Lower Ct values at isolation were observed in Omicron cases than in ancestral strain or other variants cases. No Omicron cases were detected beyond 14 days after arrival. Cases detected after 14 days of quarantine (n=58, 2.6 %) were more likely asymptomatic at isolation and had higher Ct value during isolation, some of them indicating re-positivity or post-arrival infections.

Conclusions

Testing inbound travellers at arrival and during quarantine can detect imported cases early, but may not prevent all COVID-19 introductions into the community. Public health measures should be adapted in response to the emergence of SARS-CoV-2 variants based on evidence from ongoing surveillance.

Machine learning based predictive modeling and risk factors for prolonged SARS-CoV-2 shedding

BACKGROUND

The global outbreak of the coronavirus disease 2019 (COVID-19) has been enormously damaging, in which prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, previously 2019-nCoV) infection is a challenge in the prevention and treatment of COVID-19. However, there is still incomplete research on the risk factors that affect delayed shedding of SARS-CoV-2.

METHODS

In a retrospective analysis of 56,878 hospitalized patients in the Fangcang Shelter Hospital (National Convention and Exhibition Center) in Shanghai, China, we compared patients with the duration of SARS-CoV-2 viral shedding > 12 days with those days < 12 days. The results of real-time polymerase chain reaction (RT-PCR) tests determined the duration of viral shedding from the first day of SARS-CoV-2 positivity to the day of SARS-CoV-2 negativity. The extreme gradient boosting (XGBoost) machine learning method was employed to establish a prediction model for prolonged SARS-CoV-2 shedding and analyze significant risk factors. Filtering features retraining and Shapley Additive Explanations (SHAP) techniques were followed to demonstrate and further explain the risk factors for long-term SARS-CoV-2 infection.

RESULTS

We conducted an assessment of ten different features, including vaccination, hypertension, diabetes, admission cycle threshold (Ct) value, cardio-cerebrovascular disease, gender, age, occupation, symptom, and family accompaniment, to determine their impact on the prolonged SARS-CoV-2 shedding. This study involved a large cohort of 56,878 hospitalized patients, and we leveraged the XGBoost algorithm to establish a predictive model based on these features. Upon analysis, six of these ten features were significantly associated with the prolonged SARS-CoV-2 shedding, as determined by both the importance order of the model and our results obtained through model reconstruction. Specifically, vaccination, hypertension, admission Ct value, gender, age, and family accompaniment were identified as the key features associated with prolonged viral shedding.

CONCLUSIONS

We developed a predictive model and identified six risk factors associated with prolonged SARS-CoV-2 viral shedding. Our study contributes to identifying and screening individuals with potential long-term SARS-CoV-2 infections. Moreover, our research also provides a reference for future preventive control, optimizing medical resource allocation and guiding epidemiological prevention, and guidelines for personal protection against SARS-CoV-2.

Optimization of SARS-CoV-2 culture from clinical samples for clinical trial applications

Clinical trials of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) therapeutics often include virological secondary endpoints to compare viral clearance and viral load reduction between treatment and placebo arms. This is typically achieved using quantitative reverse-transcriptase PCR (RT-qPCR), which cannot differentiate replicant competent virus from non-viable virus or free RNA, limiting its utility as an endpoint. Culture-based methods for SARS-CoV-2 exist; however, these are often insensitive and poorly standardized for use as clinical trial endpoints. We report optimization of a culture-based approach evaluating three cell lines, three detection methods, and key culture parameters. We show that Vero-angiotensin-converting enzyme 2-transmembrane serine protease 2 cells in combination with RT-qPCR of culture supernatants from the first passage provides the greatest overall detection of Delta viral replication (22 of 32, 68.8%), being able to identify viable virus in 83.3% (20 of 24) of clinical samples with initial Ct values of <30. Likewise, we demonstrate that RT-qPCR using culture supernatants from the first passage of Vero human signaling lymphocytic activation molecule cells provides the highest overall detection of Omicron viral replication (9 of 31, 29%), detecting live virus in 39.1% (9 of 23) of clinical samples with initial Ct values of <25. This assessment demonstrates that combining RT-qPCR with virological endpoint analysis has utility in clinical trials of therapeutics for SARS-CoV-2; however, techniques may require optimization based on dominant circulating strain.

IMPORTANCE

RT-qPCR is commonly used for virological endpoints during clinical trials for antiviral therapy to determine the quantity and presence of virus in a sample. However, RT-qPCR identifies viral RNA and cannot determine if viable virus is present. Existing culture-based techniques for SARS-CoV-2 are insensitive and not sufficiently standardized to be employed as clinical study endpoints. The use of a culture system to monitor replicating viruses could mitigate the possibility of molecular techniques identifying viral RNA from inactive or lysed viral particles. The methodology optimized in this study for detecting infectious viruses may have application as a secondary virological endpoint in clinical trials of therapeutics for SARS-CoV-2 in addition to numerous research processes.

Parental knowledge about respiratory syncytial virus and attitudes toward infant immunization with monoclonal antibodies in France

BACKGROUND AND AIM

Respiratory syncytial virus (RSV) is a leading cause of hospitalization of infants with respiratory infections. A new immunization using monoclonal antibodies (mAbs) may offer protection against RSV infections. A study was conducted across eight countries to gain insight into parental awareness of RSV, their sources of child health information, and attitudes toward infant immunization against RSV using mAbs. This paper presents the findings from France.

METHODS

In 2021, a survey was conducted in eight countries among expecting and current parents with children younger than 24 months of age. Eligible respondents included parents who were open to childhood immunizations, i.e., they had given or planned to give their children "all," "most," or "some" immunizations.

RESULTS

In France, the survey respondents had high adoption rates for childhood immunizations. Key drivers behind these high rates were the desire to protect their children from severe diseases and adherence to mandatory immunizations, whereas concerns about safety were the main barriers. While general practitioners and pediatricians were key sources of advice on child health, many parents also requested information about immunizations from health authorities and nurses. Sources of advice varied with parental age, gender, educational level, and income. The majority of parents had no knowledge about mAbs or passive immunization, and the overall awareness of RSV was low. When informed about RSV and mAbs, most parents held neutral to positive attitudes toward nirsevimab for their infants if recommended by a healthcare professional and/or included in the immunization program. These findings were further confirmed by the 60 %-80 % uptake rates of nirsevimab following the introduction in September 2023.

Accuracy of point-of-care SARS-CoV-2 detection using buccal swabs in pediatric emergency departments

To optimize the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children, specimen collection and testing method are crucial considerations. Ideally, specimen collection is easy and causes minimal discomfort, and the laboratory approach is simple, accurate, and rapid. In this prospective cohort study we evaluated the accuracy of a point-of care nucleic acid device using caregiver/patient self-collected buccal swabs. Participants were recruited in 14 Canadian tertiary care pediatric emergency departments. Children <18 years of age deemed to require SARS-CoV-2 testing were eligible. Caregivers or the patient-collected buccal swabs which were tested on the ABBOTT ID NOW. The reference standard was nasopharyngeal swab specimens collected by a healthcare provider tested via laboratory reverse transcription PCR (RT-PCR). We enrolled 2,640 study participants and 14.4% (381/2,640) were SARS-CoV-2 RT-PCR-positive. Eight percent (223/2,640) and 85.0% (2,244/2,640) were concordant test-positive and concordant test-negative, respectively. Sensitivity and specificity of the investigational approach were 58.5% [95% confidence interval (CI): 53.4, 63.5] and 99.3% (95% CI: 98.9, 99.6), respectively. Cycle threshold values were lower among concordant [median 17 (15, 21)] relative to discordant [median 30 (22, 35)] swabs (P < 0.001). Sensitivity was greatest among children <4 years of age, when caregivers performed the swabs, among unvaccinated children, and those with shorter symptom duration. Across multiple pain measures, less pain was associated with buccal swab testing. Although accuracy of the buccal swab point-of-care SARS-CoV-2 test was good and negative agreement was excellent, sensitivity was only 58.5%. Concordance was greater among those with higher viral loads, and the approach involving buccal swabs was less painful.IMPORTANCETo optimize the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children, specimen collection and testing method are crucial considerations. Ideally, specimen collection is easy and causes minimal discomfort, and laboratory approach is simple, accurate, and rapid. We evaluated the accuracy and pain associated with buccal swab specimen collection by caregivers or children themselves who were tested using a point-of-care isothermal nucleic acid amplification SARS-CoV-2 test. This novel approach was compared to nasopharyngeal swab specimens tested using laboratory-based PCR tests. While negative agreement was excellent, positive percent agreement was less than 60%. Concordance was greater among those with higher viral loads, and thus, sensitivity is excellent when transmissibility is more likely to occur. Importantly, the approach involving buccal swabs was significantly less painful, and thus, children and their caregivers are more likely to agree to testing using such an approach.CLINICAL TRIALSRegistered at ClinicalTrials.gov (NCT05040763).

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.

Exploring the relationship between cycle threshold values and oral manifestations in COVID-19: a comprehensive overview

OBJECTIVE

This cross-sectional study aimed to compare oral manifestations between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-positive and SARS-CoV-2-negative patients and to examine associations between oral symptoms, Ct values of E and N SARS-CoV-2 viral genes, and the implications of low Ct values indicating a high viral load, which is a predictive factor for the outcome of COVID-19.

METHODS

A total of 353 participating patients were aged ≥18 years with clinical manifestations of COVID-19 infection and tested for SARS-CoV-2 carriage at the medical center, by reverse transcriptase polymerase chain reaction (RT-PCR). All patients filled out an anonymous digital questionnaire regarding oral and general symptoms and overall medical health.  Results: A significant association was found between SARS-CoV-2 carriage and dry mouth, unpleasant taste and changes in taste (p < 0.001); for example, 37.4% of the 147 SARS-CoV-2- positive participants had a dry mouth, compared to 18.9% of the 206 SARS-CoV-2- negative participants. Oral blisters were experienced by patients with an E gene Ct value of 10-20 (50%) or 21-30 (50%) (p = 0.041). Bad breath, dry mouth, unpleasant taste and changes in taste were mostly present in participants whose Ct values of both E and N genes were between 21 and 30.  Conclusions: This study found significant associations between low Ct values of E and N SARS-CoV-2 viral genes and high viral load, indicating that Ct values can serve as predictive factors for COVID-19 outcomes. The findings suggest that while oral symptoms are present, the Ct values and associated high viral loads are more critical indicators of disease severity and prognosis.

SARS-CoV-2 viral load is linked to remdesivir efficacy in severe Covid-19 admitted to intensive care

Remdesivir therapy has been declared as efficient in the early stages of Covid-19. Of the 339 patients (males 55.8%, age 71(59;77) years) with a detectable viral load, 140 were treated with remdesivir (of those 103 in the ICU and 57 immunosuppressed) and retrospectively compared with 199 patients (of those 82 in the ICU and 28 immunosuppressed) who were denied therapy due to advanced Covid-19. The viral load was estimated by detecting nucleocapsid antigen in serum (n = 155, median 217(28;1524)pg/ml), antigen in sputum (n = 18, COI 18(4.6;32)), nasopharyngeal antigen (n = 44, COI 17(8;35)) and the real-time PCR (n = 122, Ct 21(18;27)). After adjustment for confounders, patients on remdesivir had better 12-month survival (HR 0.66 (0.44;0.98), p = 0.039), particularly when admitted to the ICU (HR 0.49 (0.29;0.81), p = 0.006). For the immunocompromised patients, the difference did not reach statistical significance (HR 0.55 (0.18;1.69), p = 0.3). The other most significant confounders were age, ICU admission, mechanical ventilation, leukocyte/lymphocyte ratio, admission creatinine and immunosuppression. The impact of monoclonal antibodies or previous vaccinations was not significant. Despite frequent immune suppression including haemato-oncology diseases, lymphopenia, and higher inflammatory markers in the remdesivir group, the results support remdesivir administration with respect to widely available estimates of viral load in patients with high illness severity.

Diagnostic performance of multiplex lateral flow tests in ambulatory patients with acute respiratory illness

We assessed the performance of three different multiplex lateral flow assays manufactured by SureScreen, Microprofit and Goldsite which provide results for influenza, respiratory syncytial virus (RSV) and SARS-CoV-2. Between 4 April and 20 October 2023, 1646 patients 6 months and older presenting to an outpatient department of a hospital in Hong Kong with ≥2 symptoms or signs of an acute respiratory illness were enrolled. The point estimates for all three multiplex tests had sensitivity >80% for influenza A and SARS-CoV-2 compared to PCR, and the tests manufactured by Microprofit and Goldsite had sensitivity >84% to detect RSV. Specificity was >97% for all three tests except for the SureScreen test which had specificity 86.2% (95% CI: 83.9% to 88.3%) for influenza A. Sensitivity was lower than reported by the manufacturers, resulting in a higher risk of false negatives. The three multiplex tests performed better in patients with high viral loads.

A single domain antibody-based Luminex assay for the detection of SARS-CoV-2 in clinical samples

Within the past decade, single domain antibodies (sdAbs) have been recognized as unique affinity binding reagents that can be tailored for performance in a variety of immunoassay formats. Luminex MagPlex color-coded magnetic microspheres provide a high-throughput platform that enables multiplexed immunoassays. We developed a MagPlex bead-based assay for the detection of SARS-CoV-2, using sdAbs against SARS-CoV-2 nucleocapsid (N) protein in which we engineered the sdAb capture reagents to orient them on the beads. The oriented sdAbs provided an increase in sensitivity over randomly oriented sdAbs for samples of N diluted in buffer, which also translated into better detection of SARS-CoV-2 in clinical samples. We assessed the specificity of the assay by examining seasonal coronavirus clinical samples. In summary, we provide a proof-of-concept that a bead-based assay using sdAbs to detect SARS-CoV-2 is feasible and future research combining it with other sdAb-coated beads that can detect other viruses may provide a useful diagnostic tool.

Trends in SARS-CoV-2 Cycle Threshold Values in Bosnia and Herzegovina-A Retrospective Study

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to the COVID-19 pandemic, has significantly impacted global public health. The proper diagnosis of SARS-CoV-2 infection is essential for the effective control and management of the disease. This study investigated the SARS-CoV-2 infection using RT-qPCR tests from laboratories in Bosnia and Herzegovina. We performed a retrospective study of demographic data and Ct values from 170,828 RT-qPCR tests from April 2020 to April 2023, representing 9.3% of total national testing. Samples were collected from 83,413 individuals across different age groups. Of all tests, 33.4% were positive for SARS-CoV-2, with Ct values and positivity rates varying across demographics and epidemic waves. The distribution was skewed towards older age groups, although lower positivity rates were observed in younger age groups. Ct values, indicative of viral load, ranged from 12.5 to 38. Lower Ct values correlated with higher positive case numbers, while higher Ct values signaled outbreak resolution. Additionally, Ct values decreased during epidemic waves but increased with the dominance of certain variants. Ct value-distribution has changed over time, particularly after the introduction of SARS-CoV-2 variants of interest/concern. Established Ct value trends might, therefore, be used as an early indicator and additional tool for informed decisions by public health authorities in SARS-CoV-2 and future prospective pandemics. Moreover, they should not be overlooked in future epidemiological events.

Future worldwide coronavirus disease 2019 epidemic predictions by Gaidai multivariate risk evaluation method

Accurate estimation of pandemic likelihood in every US state of interest and at any time. Coronavirus disease 2019 (COVID-19) is an infectious illness with a high potential for global dissemination and low rates of fatality and morbidity, placing some strains on national public health systems. This research intends to benchmark a novel technique, that enables hazard assessment, based on available clinical data, and dynamically observed patient numbers while taking into account pertinent territorial and temporal mapping. Multicentre, population-based, and biostatistical strategies have been utilized to process raw/unfiltered medical survey data. The expansion of extreme value statistics from the univariate to the bivariate situation meets with numerous challenges. First, the univariate extreme value types theorem cannot be directly extended to the bivariate (2D) case,-not to mention challenges with system dimensionality higher than 2D. Assessing outbreak risks of future outbreaks in any nation/region of interest. Existing bio-statistical approaches do not always have the benefits of effectively handling large regional dimensionality and cross-correlation between various regional observations. These methods deal with temporal observations of multi-regional phenomena. Apply contemporary, novel statistical/reliability techniques directly to raw/unfiltered clinical data. The current study outlines a novel bio-system hazard assessment technique that is particularly suited for multi-regional environmental, bio, and public health systems, observed over a representative period. With the use of the Gaidai multivariate hazard assessment approach, epidemic outbreak spatiotemporal risks may be properly assessed. Based on raw/unfiltered clinical survey data, the Gaidai multivariate hazard assessment approach may be applied to a variety of public health applications. The study's primary finding was an assessment of the risks of epidemic outbreaks, along with a matching confidence range. Future global COVID-19/severe acute respiratory syndrome coronavirus 2 (SARS-COV2) epidemic risks have been examined in the current study; however, COVID-19/SARS-COV2 infection transmission mechanisms have not been discussed.

Deisolation in the Healthcare Setting Following Recent COVID-19 Infection

BACKGROUND

Deisolation of persons infected with SARS-CoV-2, the virus that causes COVID-19, presented a substantial challenge for healthcare workers and policy makers, particularly during the early phases of the pandemic. Data to guide deisolation of SARS-CoV-2-infected patients remain limited, and the risk of transmitting and acquiring infection has changed with the evolution of SARS-CoV-2 variants and population immunity from previous vaccination or infection, or both.

AIMS

This review examines the evidence to guide the deisolation of SARS-CoV-2-infected inpatients within the hospital setting when clinically improving and also of healthcare workers with COVID-19 prior to returning to work.

METHODS

A review was performed using relevant search terms in Medline, EMBASE, Google Scholar, and PubMed.

RESULTS AND DISCUSSION

The evidence is reviewed with regards to the nature of SARS-CoV-2 transmission, the role of testing to guide deisolation, and the impact of SARS-CoV-2-specific immunity. A paradigm and recommendations are proposed to guide deisolation for inpatients and return to work for healthcare workers.

SARS-CoV-2 Polymerase Chain Reaction Cycle Threshold Trends in Patients Who Are Immunocompromised and Implications for Isolation Precautions

Among 495 patients who were immunocompromised and tested positive for SARS-CoV-2, polymerase chain reaction cycle thresholds remained <33 beyond 20 days more frequently in patients with hematologic malignancies, particularly those receiving B-cell-depleting or Bruton tyrosine kinase inhibitor therapy, as compared with those with solid organ malignancy (26% vs 5%).

SARS-CoV-2 RT-PCR as a universal screening on planned admission in asymptomatic patients

Universal screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on admission is reportedly beneficial in preventing nosocomial infections. However, some issues remain, including low positivity rate, cost, and time required for testing. We describe SARS-CoV-2 reverse transcription polymerase chain reaction (PCR) for universal screening in asymptomatic patients on planned admissions. In total, 14,574 patients were included between October 12, 2020, and June 23, 2022. The PCR-positive rate for the period was 0.44 % (64/14,574). The PCR positivity for the epidemic period by strain was 0.28 % (95 % confidence interval [CI] 0.12-0.56 %), 0.16 % (95 % CI 0.05-0.37 %), 0.21 % (95 % CI 0.09-0.41 %), and 0.9 % (95 % CI 0.65-1.2 %) for the wild-type strain, Alpha, Delta, and Omicron variants, respectively. The proportion of Ct values < 30 was higher in the first half of the epidemic (first vs. second, 29.4 % [95 % CI 16.9-44.8 %] vs. 16.7 % [95 % CI 6.0-28.5 %]), whereas that of Ct values ≥ 35 increased significantly in the second half (first vs. second, 32.4 % [95 % CI 19.3-47.8 %] vs. 70.0 % [95 % CI 53.5-83.4 %]). Of all positives, 50 % (32/64) had a coronavirus disease (COVID-19) history before PCR screening, with a median of 28 days (10-105) from COVID-19 onset or positive to PCR screening. PCR screening may help detect positives with high viral loads early in the epidemic for each mutant strain, with an increasing proportion of positives with low viral loads later in the epidemic. PCR testing may be unnecessary for recently diagnosed cases and patients in whom reinfection is unlikely.

Performance of two rapid antigen tests against SARS-CoV-2 in neighborhoods of socioeconomic vulnerability from a middle-income country

BACKGROUND

As new and improved antigen-detecting rapid diagnostic tests for SARS-CoV-2 infection (Ag-RDT) continue to be developed, assessing their diagnostic performance is necessary to increase test options with accurate and rapid diagnostic capacity especially in resource-constrained settings. This study aimed to assess the performance of two Ag-RDTs in a population-based study.

METHODS

We conducted a diagnostic accuracy study in neighborhoods with high socioeconomic vulnerability in Salvador-Brazil, including individuals aged ≥12 years old who attended primary health services, between July and December 2022, with COVID-19 symptoms or who had been in contact with a confirmed case. Two Ag-RDTs were compared in parallel using reverse transcription polymerase chain reaction (RT-PCR) as reference standard, the PanbioTM COVID-19 Ag test (Abbott®) and Immuno-Rapid COVID-19 Ag (WAMA Diagnostic®). Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) were calculated.

RESULTS

For the Abbott test the sensitivity was 52.7% (95% CI: 44.3% - 61.0%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.4% (95% CI: 75.9% - 84.4%). For the WAMA test, the sensitivity was 53.4% (95% CI: 45.0% - 61.6%), specificity 100% (95% CI: 98.7% - 100%), PPV 100% (95% CI: 95.4% - 100%) and NPV 80.7% (95% CI: 76.2% - 84.6%). Sensitivity for the group with Cycle Threshold (CT) <24 was 82.3% (95%CI: 72.1-90.0, n = 83) for PanbioTM COVID-19 Ag test and 87.3% (95%CI: 77.9-93.8, n = 83) for Immuno-Rapid COVID-19 Ag test.

CONCLUSION

Sensitivity for both Ag-RDT was lower than reported by manufacturers. In the stratified analysis, sensitivity was higher among those with lower CT values <24. Specificity was high for both rapid antigen tests. Both Ag-RDT showed to be useful for rapid diagnostic of potential cases of COVID-19. Negative results must be assessed carefully according to clinical and epidemiological information.

A retrospective analysis of the influencing factors of nucleic acid CT value fluctuation in COVID-19 patients infected with Omicron variant virus in Changchun city

Objective

This study aimed to determine the risk factors associated with fluctuations in nucleic acid CT values in patients infected with the Omicron variant during an outbreak at a hospital in Changchun city.

Methods

A retrospective analysis was conducted on general information, medical history, vaccination history, and laboratory test data of COVID-19 patients infected with the Omicron variant and admitted to the hospital in Changchun from March 2022 to April 2022. The study aimed to explore the factors influencing nucleic acid CT value fluctuations in COVID-19 patients infected with the Omicron variant in Changchun city.

Results

Fluctuations in nucleic acid CT values were significantly correlated with occupation composition (p = 0.030), hospital stay duration (p = 0.000), heart rate (p = 0.026), creatinine (p = 0.011), platelet count (p = 0.000), glutamic-pyruvic transaminase (p = 0.045), and glutamic oxaloacetic transaminase (p = 0.017). Binary logistic regression analysis revealed significant correlations between hospital stay duration (p = 0.000), platelet count (p = 0.019), heart rate (p = 0.036), and nucleic acid CT value fluctuations (p < 0.05), indicating that they were independent risk factors. Red blood cell count was identified as a factor influencing nucleic acid CT value fluctuations in Group A patients. Occupation composition, direct bilirubin, and platelet count were identified as factors influencing nucleic acid CT value fluctuations in Group B patients. Further binary logistic regression analysis indicated that occupational composition and direct bilirubin are significant independent factors for nucleic acid CT value fluctuations in Group B patients, positively correlated with occupational risk and negatively correlated with direct bilirubin.

Conclusion

Therefore, enhancing patients' immunity, increasing physical exercise to improve myocardial oxygen consumption, reducing the length of hospital stays, and closely monitoring liver function at the onset of hospitalization to prevent liver function abnormalities are effective measures to control fluctuations in nucleic acid CT values.

Testing for SARS-CoV-2: lessons learned and current use cases

SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.

Early initiation of combined therapy in severely immunocompromised patients with COVID-19: a retrospective cohort study

This single-centre retrospective cohort study reports on the results of a descriptive (non-comparative) retrospective cohort study of early initiation of antivirals and combined monoclonal antibody therapy (mAbs) in 48 severely immunocompromised patients with COVID-19. The study assessed the outcomes and the duration of viral shedding. The patients started early combined therapy (ECT) a median of 2 days (interquartile range [IQR]: 1-3 days) after the diagnosis of SARS-CoV-2 infection. Except for 1 patient who died due COVID-19-related respiratory failure, patients had their first negative nasopharyngeal swab result after a median of 11 days (IQR: 6-17 days) after starting combined therapy. There were no reports of severe side effects. During a follow-up period of 512 days (interquartile range [IQR]: 413-575 days), 6 patients (12.5%) died and 16 (33.3%) were admitted to hospital. Moreover, 12 patients (25%) were diagnosed with SARS-CoV-2 reinfection a median of 245 days (IQR: 138-401 days) after starting combined treatment. No relapses were reported. Although there was no comparison group, these results compare favourably with the outcomes of severely immunocompromised patients with COVID-19 reported in the literature.

Early outcomes of lung transplantation with lung allografts from coronavirus disease 2019 (COVID-19)-positive donors

OBJECTIVE

Coronavirus disease 2019 (COVID-19) can be detected for extended periods of time with nucleic acid amplification test even after transmissibility becomes negligible. Lung allografts from COVID-19-positive donors have been used for transplantation in highly selected cases. This study aimed to clarify the early outcomes of lung transplantation with COVID-19-positive donors.

METHODS

The Organ Procurement and Transplantation Network/United Network for Organ Sharing database between April 2020 and June 2022 was retrospectively analyzed.

RESULTS

In the study period, 1297 COVID-19-positive donors were identified and the lungs were transplanted from 47 donors (3.6%). Of 47 donors, 44 donors were positive for COVID-19 NAT with nasopharyngeal swabs and the other 3 were positive with bronchoalveolar lavage. The COVID-19-positive lung donors were younger than the COVID-19-negative donors (28.4 ± 11.6 years vs 35.4 ± 13.6 years, P < .001). Recipients of the COVID-19-positive lungs (n = 47) were more likely have a greater lung allocation score (57.1 ± 22.9 vs 50.5 ± 19.7, P = .057) than recipients of COVID-19-negative lungs (n = 5501). The posttransplant length of hospital stay (39.8 ± 43.6 days vs 30.6 ± 34.5 days, P = .181), need for extracorporeal membrane oxygenation support at 72 hours after transplantation (2.6% [1/38] vs 10.4% [541/5184], P = .18), and 1-year overall survival rate (85.6% vs 87.1%, P = .63) were comparable between the 2 groups.

CONCLUSIONS

Carefully selected lung allografts from COVID-19-positive donors had comparable early posttransplant outcomes to lung allografts from COVID-19-negative donors.

Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections

In this study in silico a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted. The stimulation ability of the humoral immunity for each peptide was evaluated. Finally, in silico cloning was performed to develop an expression strategy for each peptide. These four peptides have suitable immunogenicity, appropriate construct, and the ability to be expressed in E.coli. These results must be experimentally validated in vitro and in vivo to ensure the immunogenicity of the kit.Communicated by Ramaswamy H. Sarma.

Evaluation of the analytical and clinical performance of two RT-PCR based point-of-care tests; Cepheid Xpert® Xpress CoV-2/Flu/RSV plus and SD BioSensor STANDARD™ M10 Flu/RSV/SARS-CoV-2

BACKGROUND

Rapid and accurate detection of viral respiratory infections is important for infection control measures. This study compares the analytical and clinical performance of the Xpert® Xpress CoV-2/Flu/RSV plus test ("Xpert", Cepheid) and the STANDARD™ M10 Flu/RSV/SARS-CoV-2 test ("M10", SD Biosensor). Both tests are quadruplex RT-PCR assays for rapid diagnosis of SARS-CoV-2, influenza A/B and RSV.

STUDY DESIGN

Analytical sensitivities were determined by limit of detection for SARS-CoV-2, influenza A, influenza B and RSV, respectively. Additionally, the clinical performance of the Xpert and the M10 tests was evaluated against standard-of-care RT-PCR by testing of 492 clinical specimens.

RESULTS

The analytical sensitivities for Xpert versus M10 test was 10, 50, 50 and 300 versus 300, 200, 800 and 1500 copies/mL for SARS-CoV-2, influenza A, influenza B and RSV, respectively. Clinical sensitivity for the Xpert test was superior across all four pathogens compared to the M10 test. Xpert showed clinical sensitivity of 100 % in all Ct-ranges for all four pathogens whereas M10 showed clinical sensitivity of 100 % in the 25-30 Ct-range, 84-100 % in the 30-35 Ct-range and 47-67 % in the >35 Ct-range across the four pathogens. Translating into real-life clinical sensitivity, the Xpert would detect 100 % of all four pathogens, whereas M10 would detect 92.1, 92.4, 84.8 and 94.7 % for SARS-CoV-2, influenza A, influenza B and RSV.

CONCLUSION

This study demonstrates improved analytical and clinical performance of Xpert Xpress CoV-2/Flu/RSV plus compared to STANDARD M10 Flu/RSV/SARS-CoV-2, which is important for ensuring accuracy of diagnosis at all stages of a respiratory infection.

Kinetics of SARS-CoV-2 infection biomarkers in a household transmission study

SARS-CoV-2 is the causative agent of COVID-19. Timely and accurate diagnostic testing is vital to contain the spread of infection, reduce delays in treatment and care, and inform patient management. Optimal specimen type (e.g. nasal swabs or saliva), timing of sampling, viral marker assayed (RNA or antigen), and correlation with viral infectivity and COVID-19 symptoms severity remain incompletely defined. We conducted a field study to evaluate SARS-CoV-2 viral marker kinetics starting from very early times after infection. We measured RNA and antigen levels in nasal swabs and saliva, virus outgrowth in cell culture from nasal swabs, and antibody levels in blood in a cohort of 30 households. Nine household contacts (HHC) became infected with SARS-CoV-2 during the study. Viral RNA was detected in saliva specimens approximately 1-2 days before nasal swabs in six HHC. Detection of RNA was more sensitive than of antigen, but antigen detection was better correlated with culture positivity, a proxy for contagiousness. Anti-nucleocapsid antibodies peaked one to three weeks post-infection. Viral RNA and antigen levels were higher in specimens yielding replication competent virus in cell culture. This study provides important data that can inform how to optimally interpret SARS-CoV-2 diagnostic test results.

A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test

OBJECTIVES

Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies.

METHODS

The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein.

RESULTS

SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002).

CONCLUSIONS

Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.

The CoLab score is associated with SARS-CoV-2 viral load during admission in individuals admitted to the intensive care unit: the CoLaIC cohort study

OBJECTIVES

The present study examines the temporal association between the changes in SARS-CoV-2 viral load during infection and whether the CoLab-score can facilitate de-isolation.

METHODS

Nasal swabs and blood samples were collected from ICU-admitted SARS-CoV-2 positive patients at Maastricht UMC+ from March 25, 2020 to October 1, 2021. The CoLab-score was calculated based on 10 blood parameters and age and can range from -43 to 6. Three mixed effects analyses compared patient categories based on initial PCR Ct values (low; Ct≤20, mid; 20>Ct≤30, high; Ct>30), serial PCR Ct values to CoLab-scores over time, and the association between within-patient delta Ct values and CoLab-scores.

RESULTS

In 324 patients, the median Ct was 33, and the median CoLab-score was -1.78. Mid (n=110) and low (n=41) Ct-categories had higher CoLab-scores over time (+0.60 points, 95 % CI; 0.04-1.17, and +0.28 points, 95 % CI -0.49 to 1.04) compared to the high Ct (n=87) category. Over time, higher serial Ct values were associated with lower serial CoLab-scores, decreasing by -0.07 points (95 % CI; -0.11 to -0.02) per day. Increasing delta Ct values were associated with a decreasing delta CoLab-score of -0.12 (95 % CI; -0.23; -0.01).

CONCLUSIONS

The study found an association between lower viral load on admission and reduced CoLab-score. Additionally, a decrease in viral load over time was associated with a decrease in CoLab-score. Therefore, the CoLab-score may make patient de-isolation an option based on the CoLab-score.

Kinetics of SARS-CoV-2 Viral Load in Hospitalized Patients

The rapid and accurate detection of infectious people is crucial in controlling outbreaks. The aim of this study was to evaluate the kinetics of the viral load expressed as Ct in COVID-19 hospitalized patients. Nasopharyngeal swab specimens were collected for RT-PCR testing. Forty-one subjects were recruited, of which 48.8% developed severe symptoms and 51.2% showed milder symptoms. The distribution of Ct values measured from the symptom onset showed that the kinetics of the viral load decreased with increasing time. A Ct of 25 (high viral load) was reached after a mean of 9.9 ± 4.8 days from the symptom onset, without a significant difference between patients with severe (10.9 ± 5.7 days) and milder (9.0 ± 3.9 days) symptoms. In 65.8% of cases, a high viral load was maintained for more than 7 days from the symptom onset, especially in patients with severe symptoms (70.6%). A Ct of 30 (moderate viral load) and of 38 (low viral load) were reached after a mean of 16.1 ± 8.1 and 28.5 ± 22.4 days from the symptom onset, respectively, with a significant difference between patients with severe (Ct = 30:17.9 ± 9.8 days; Ct = 38:34.6 ± 29.6 days) and milder (Ct = 30:14.3 ± 5.8 days; Ct = 38:22.7 ± 9.9 days) symptoms. These results provide an understanding of the viral kinetics of SARS-CoV-2 and have implications for pandemic control strategies and practices.

Differential Viral Dynamics by Sex and Body Mass Index During Acute SARS-CoV-2 Infection: Results From a Longitudinal Cohort Study

BACKGROUND

There is evidence of an association of severe coroanavirus disease (COVID-19) outcomes with increased body mass index (BMI) and male sex. However, few studies have examined the interaction between sex and BMI on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral dynamics.

METHODS

Participants conducted RT-PCR testing every 24-48 hours over a 15-day period. Sex and BMI were self-reported, and Ct values from E-gene were used to quantify viral load. Three distinct outcomes were examined using mixed-effects generalized linear models, linear models, and logistic models, respectively: all Ct values (model 1), nadir Ct value (model 2), and strongly detectable infection (at least 1 Ct value ≤28 during their infection) (model 3). An interaction term between BMI and sex was included, and inverse logit transformations were applied to quantify the differences by BMI and sex using marginal predictions.

RESULTS

In total, 7988 participants enrolled in this study and 439 participants (model 1) and 309 (models 2 and 3) were eligible for these analyses. Among males, increasing BMI was associated with lower Ct values in a dose-response fashion. For participants with BMIs greater than 29 kg/m2, males had significantly lower Ct values and nadir Ct values than females. In total, 67.8% of males and 55.3% of females recorded a strongly detectable infection; increasing proportions of men had Ct values <28 with BMIs of 35 and 40 kg/m2.

CONCLUSIONS

We observed sex-based dimorphism in relation to BMI and COVID-19 viral load. Further investigation is needed to determine the cause, clinical impact, and transmission implications of this sex-differential effect of BMI on viral load.

A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic

Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.

Antiviral and Monoclonal Antibody Combination Therapy in Haematological Patients in the Omicron Era

Abstract: Im We describe here a single-center case series of 27 IC COVID-19 inpatients (mostly with haematological disorders) treated with a combined therapy based on tixagevimab/cilgavimab (T/C) plus small-molecule antivirals (AV), between April 1 2022 and November 30 2022.  Keywords: immunocompromised; SARS-CoV-2 infection; monoclonal antibodies; antivirals; persistent infection; viral evolution

Diagnostic performance of rapid antigen testing for SARS-CoV-2: the COVid-19 AntiGen (COVAG) extension study

Background

This study is the extension of the COVAG study. We compared two RATs, the Panbio COVID-19 Ag Rapid Test (Abbott) and the SD Biosensor Q SARS-CoV-2 Rapid Antigen Test (Roche), against RT-PCR on the foil of new variants.

Methods

We included 888 all-comers at a diagnostic center between October 20, 2021, and March 18, 2022. RT-PCR-positive samples with a Ct value ≤32 were examined for SARS-CoV-2 variants.

Findings

The sensitivity of the Abbott-RAT and Roche-RAT were 65 and 67%, respectively. For both RATs, lower Ct values were significantly correlated with higher sensitivity. For samples with Ct values ≤25, the sensitivities of the Roche-RAT and of the Abbott-RAT were 96 and 95%, for Ct values 25-30 both were 19%, and for Ct values ≥30 they were 6 and 2%, respectively. The RATs had substantially higher sensitivities in symptomatic than asymptomatic participants (76, 77%, vs. 29, 31%, for Abbott-RAT, Roche-RAT, respectively) and in participants referred to testing by their primary care physician (84, 85%) compared to participants who sought testing due to referral by the health department (55, 58%) or a warning by the Corona-Warn-App (49, 49%). In persons with self-reported previous COVID-19 sensitivities were markedly lower than in patients without previous COVID-19: 27% vs. 75% for Roche-RAT and 27% vs. 73% for Abbott-RAT. We did not find significant correlation between vaccination status and sensitivity. The Omicron variant was detected with a sensitivity of 94 and 92%, the delta variant with a sensitivity of 80 and 80% for Abbott-RAT and Roche-RAT, respectively. This difference is attributable to the lower Ct values of the Omicron samples compared to the Delta samples. When adjusted for the Ct value, a multivariate logistic regression did not show a significant difference between Omicron and Delta. In terms of sensitivity, we found no significant difference between the wild-type and the Omicron and Delta variants, but a significantly lower sensitivity to the alpha variant compared to the other variants.The specificities were > 99% overall.