Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR

Disposable graphene-oxide screen-printed electrode integrated with portable device for detection of SARS-CoV-2 in clinical samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis is the need of the hour, as cases are persistently increasing, and new variants are constantly emerging. The ever-changing nature of the virus leading to multiple variants, has brought an imminent need for early, accurate and rapid detection methods. Herein, we have reported the design and fabrication of Screen-Printed Electrodes (SPEs) with graphene oxide (GO) as working electrode and modified with specific antibodies for SARS-CoV-2 Receptor Binding Domain (RBD). Flexibility of design, and portable nature has made SPEs the superior choice for electrochemical analysis. The developed immunosensor can detect RBD as low as 0.83 fM with long-term storage capacity. The fabricated SPEs immunosensor was tested using a miniaturized portable device and potentiostat on 100 patient nasopharyngeal samples and corroborated with RT-PCR data, displayed 94 % sensitivity. Additionally, the in-house developed polyclonal antibodies detected RBD antigen of the mutated Omicron variant of SARS-CoV-2 successfully. We have not observed any cross-reactivity/binding of the fabricated immunosensor with MERS (cross-reactive antigen) and Influenza A H1N1 (antigen sharing common symptoms). Hence, the developed SPEs sensor may be applied for bedside point-of-care diagnosis of SARS-CoV-2 using miniaturized portable device, in clinical samples.

Tunable nanofluidic device for digital nucleic acid analysis

Nano/microfluidic-based nucleic acid tests have been proposed as a rapid and reliable diagnostic technology. Two key steps for many of these tests are target nucleic acid (NA) immobilization followed by an enzymatic reaction on the captured NAs to detect the presence of a disease-associated sequence. NA capture within a geometrically confined volume is an attractive alternative to NA surface immobilization that eliminates the need for sample pre-treatment (e.g. label-based methods such as lateral flow assays) or use of external actuators (e.g. dielectrophoresis) that are required for most nano/microfluidic-based NA tests. However, geometrically confined spaces hinder sample loading while making it challenging to capture, subsequently, retain and simultaneously expose target NAs to required enzymes. Here, using a nanofluidic device that features real-time confinement control via pneumatic actuation of a thin membrane lid, we demonstrate the loading of digital nanocavities by target NAs and exposure of target NAs to required enzymes/co-factors while the NAs are retained. In particular, as proof of principle, we amplified single-stranded DNAs (M13mp18 plasmid vector) in an array of nanocavities via two isothermal amplification approaches (loop-mediated isothermal amplification and rolling circle amplification).

Usefulness of receptor binding domain protein-based serodiagnosis of COVID-19

Objectives

This study evaluated the performance of recombinant receptor binding domain (RBD) protein-based enzyme-linked immunosorbent assays (RBD-ELISAs) for detecting anti-SARS-CoV-2 immunoglobulin (Ig) G and IgM antibodies.

Methods

In this study, 705 sera from SARS-CoV-2-infected individuals and 315 sera from healthy individuals were analyzed.

Results

The RBD-ELISA IgG exhibited high specificity (99.1%) and moderate sensitivity (48.0%), with an overall diagnostic accuracy of 73.5%. RBD-ELISA IgM demonstrated specificity at 94.6% and sensitivity at 51.1%, with an accuracy of 72.8%. Both assays displayed improved performance when analyzing samples collected 15-21 days post-symptom onset, achieving sensitivity and accuracy exceeding 88% and 90%, respectively. Combining RBD-ELISA IgG and IgM in parallel analysis enhanced sensitivity to 98.6% and accuracy to 96.2%. Comparing these RBD-ELISAs with commercially available tests, the study found overlapping sensitivity and similar specificity values. Notably, the combined RBD-ELISA IgG and IgM showed superior performance. Cross-reactivity analysis revealed low false-positive rates (4.4% for IgG, 3.7% for IgM), primarily with viral infections.

Conclusion

This research underscores the potential of RBD-based ELISAs for COVID-19 diagnosis, especially when assessing samples collected 15-21 days post-symptom onset and utilizing a parallel testing approach. The RBD protein's immunogenicity and specificity make it a valuable tool for serodiagnosis, offering an alternative to polymerase chain reaction-based methods, particularly in resource-limited settings.

Robotic system for nasopharyngeal swab sampling based on remote center of motion mechanism

PURPOSE

In this study, a robotic system is proposed for nasopharyngeal (NP) swab sampling with high safety and efficiency. Most existing swab-sampling robots have more than six degrees of freedom (DOFs). However, not all six DOFs are necessarily required for NP swab sampling. A high number of DOFs can cause safety problems, such as collisions between the robot and patient.

METHOD

We developed a new type of robot with four DOFs for NP swab sampling that consists of a two DOFs remote center of motion (RCM) mechanism, a two DOFs insertion mechanism, and a nostril support unit. With the nostril support unit, the robot no longer needs to adjust the insertion position of the swab. The proposed robot enables the insertion orientation and depth to be adjusted according to different postures or facial shapes of the subject. For intuitive and precise remote control of the robot, a dedicated master device for the RCM and a visual feedback system were developed.

RESULT

The effectiveness of the robotic system was demonstrated by repeatability, RCM accuracy, tracking accuracy, and in vitro phantom experiments. The average tracking error between the master device and the robot was less than 2 mm. The contact force exerted on the swab prior to reaching the nasopharynx was less than 0.04 N, irrespective of the phantom's pose.

CONCLUSION

This study confirmed that the RCM-based robotic system is effective and safe for NP swab sampling while using minimal DOFs.

Enhancing COVID-19 CT Image Segmentation: A Comparative Study of Attention and Recurrence in UNet Models

Imaging plays a key role in the clinical management of Coronavirus disease 2019 (COVID-19) as the imaging findings reflect the pathological process in the lungs. The visual analysis of High-Resolution Computed Tomography of the chest allows for the differentiation of parenchymal abnormalities of COVID-19, which are crucial to be detected and quantified in order to obtain an accurate disease stratification and prognosis. However, visual assessment and quantification represent a time-consuming task for radiologists. In this regard, tools for semi-automatic segmentation, such as those based on Convolutional Neural Networks, can facilitate the detection of pathological lesions by delineating their contour. In this work, we compared four state-of-the-art Convolutional Neural Networks based on the encoder-decoder paradigm for the binary segmentation of COVID-19 infections after training and testing them on 90 HRCT volumetric scans of patients diagnosed with COVID-19 collected from the database of the Pisa University Hospital. More precisely, we started from a basic model, the well-known UNet, then we added an attention mechanism to obtain an Attention-UNet, and finally we employed a recurrence paradigm to create a Recurrent-Residual UNet (R2-UNet). In the latter case, we also added attention gates to the decoding path of an R2-UNet, thus designing an R2-Attention UNet so as to make the feature representation and accumulation more effective. We compared them to gain understanding of both the cognitive mechanism that can lead a neural model to the best performance for this task and the good compromise between the amount of data, time, and computational resources required. We set up a five-fold cross-validation and assessed the strengths and limitations of these models by evaluating the performances in terms of Dice score, Precision, and Recall defined both on 2D images and on the entire 3D volume. From the results of the analysis, it can be concluded that Attention-UNet outperforms the other models by achieving the best performance of 81.93%, in terms of 2D Dice score, on the test set. Additionally, we conducted statistical analysis to assess the performance differences among the models. Our findings suggest that integrating the recurrence mechanism within the UNet architecture leads to a decline in the model's effectiveness for our particular application.

COVID-19 detection prior to motility examinations: Prospective evaluation of pre-test questionnaires and PCR-testing

BACKGROUND/AIMS

COVID-19 pandemic has produced an increased burden for motility laboratories due to the need to implement measures to minimize infection risk during examinations. International Societies have proposed algorithms for evaluation of active infection risk using symptom questionnaires or performing COVID-19 specific detection tests. The aim of the present study is to evaluate prospectively the independent value of a symptom-based questionnaire and RT-PCR test to detect COVID-19 infection before a digestive motility examination.

PATIENTS/METHODS

All patients referred for a motility study during a 4 month period with high incidence of COVID-19 in the community were prospectively evaluated with a symptom-questionnaire administered by phone one week before the examination, and a PCR test performed 48h before the examination, following international guidelines recommendations.

RESULTS

The symptom questionnaire could be obtained from 435 patients, 7 patients referred COVID-19 symptoms, but only 1 of them had a positive PCR. From 481 PCR tests performed, 8 were positive. Only 1 patient had reported symptoms in the previous questionnaire, and 2 additional patients developed COVID-19 symptoms later. Hence, 435 telephonic questionnaires should be done for one COVID-19 case detection (detection tax 0.22%); and 60 PCR should be performed for one COVID-19 case detection (detection tax 1.66%).

CONCLUSIONS

The use of screening strategies prior to a motility exploration results in a low rate of infection detection, especially the use of subjective symptom questionnaires, and the correct protection measures during motility explorations with aerosol generation remain the cornerstone to prevent COVID-19 infections.

CRISPR/Cas and Argonaute-Based Biosensors for Pathogen Detection

Over the past few decades, pathogens have posed a threat to human security, and rapid identification of pathogens should be one of the ideal methods to prevent major public health security outbreaks. Therefore, there is an urgent need for highly sensitive and specific approaches to identify and quantify pathogens. Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas systems and Argonaute (Ago) belong to the Microbial Defense Systems (MDS). The guided, programmable, and targeted activation of nucleases by both of them is leading the way to a new generation of pathogens detection. We compare these two nucleases in terms of similarities and differences. In addition, we discuss future challenges and prospects for the development of the CRISPR/Cas systems and Argonaute (Ago) biosensors, especially electrochemical biosensors. This review is expected to afford researchers entering this multidisciplinary field useful guidance and to provide inspiration for the development of more innovative electrochemical biosensors for pathogens detection.

M gene targeted qRT-PCR approach for SARS-CoV-2 virus detection

Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.

Diagnostic Performance Between Chest CT Severity Score and Initial Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Cycle Values in COVID-19 Patients and Their Relation With the Clinical Status of Patients

INTRODUCTION

Reverse transcription-polymerase chain reaction (RT-PCR) is used as a standard test for the diagnosis of SARS-CoV-2 viral RNA from nasopharyngeal aspirates. However, this method lacks sensitivity and cannot assess disease severity. A CT scan of the thorax provides a CT severity score (CT-SS), which depicts lung involvement and disease severity. This study aims to investigate the diagnostic value of chest CT compared with RT-PCR cycle threshold (Ct) values in COVID-19 and relate it clinically with the disease severity of patients.

METHODS

This retrospective observational study was conducted in a tertiary center from April 2021 to March 2022. We included 511 patients who had tested RT-PCR positive for COVID-19, were hospitalized, and had undergone high-resolution CT (HRCT) thorax. Data was collected from patient records regarding name, age, sex, admission data, baseline investigations including Ct value, management, and outcome. HRCT was reviewed to assess lung involvement and calculate CT-SS. Data was analyzed using SPSS Statistics version 25 (IBM Corp. Released 2017. IBM SPSS Statistics for Windows, Version 25.0. Armonk, NY: IBM Corp.).

RESULT

The mean age of patients was 50.4 ± 13.7 years, and the majority (67.5%) were male. Gender-wise, there was no difference in RT-PCR cycle threshold (Ct) values; however, CT-SS was significantly higher in males (17.5 ± 4.8 vs.10.5 ± 6.6, t=-13.6, p<0.0001). ICU admission was needed for 34.8% of patients, and they had a significantly lower Ct value (21.7 ± 3.3 vs. 22.8 ± 3.7, t=21.10, p<0.0001) and higher CT-SS (16.3 ± 4.5 vs. 6.7 ± 5.1, t=-3.32, p=0.001).

CONCLUSION

Ct values could not differentiate between moderate and severe patients. CT-SS was not related to the viral load at admission. Patients who succumbed had significantly lower Ct values and higher CT-SS.

Coinfection of SARS-CoV-2 and influenza A (H3N2) detected in bronchoalveolar lavage fluid of a patient with long COVID using metagenomic next-generation sequencing: a case report

The growing number of long COVID cases has drawn clinical attention to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has been spreading worldwide since winter 2019. Its symptoms are not limited to fatigue and shortness of breath but also affect daily life. We report the use of metagenomic next-generation sequencing (mNGS) to detect coinfection with SARS-CoV-2 and influenza A virus in a patient with long COVID. The patient was admitted with fever, expectoration, fatigue, and shortness of breath. The PCR test was negative due to possible clearance of SARS-Cov-2 in the upper respiratory tract of patients with long COVID. Other routine microbiological tests were also negative, making the clinical diagnosis difficult. Bronchoalveolar lavage fluid (BALF) samples were tested using mNGS. The patient was diagnosed and treated promptly, recovered quickly, and continued taking azvudine after discharge; his condition was stable. This study illustrates that mNGS may be valuable for the timely diagnosis of patients with long COVID and their mixed infections.

Novel Label-Free Nanocrystalline Gold Interdigitated Microelectrode Immunosensor for the Rapid and Ultrasensitive Detection of SARS-CoV-2

Waves of COVID-19 outbreaks have dragged down the global economy and endangered human life. There is an urgent need for timeliness and sensitive SARS-CoV-2 detection techniques to complement the existing PCR assay. Herein, the controllable growth of gold crystalline grains was achieved by applying the reverse current during pulse electrochemical deposition (PED) interval. The proposed method validates the effects of pulse reverse current (PRC) on the atomic arrangement, crystal structures, orientations, and film characteristics in Au PED. The gap between the gold grains on the surface of the nanocrystalline gold interdigitated microelectrodes (NG-IDME) fabricated by the PED+PRC process matches the size of the antiviral antibody. Immunosensors are prepared by binding a large number of antiviral antibodies on the surface of NG-IDME. The NG-IDME immunosensor has a high specific capture ability for SARS-CoV-2 nucleocapsid protein (SARS-CoV-2/N-Pro) and completes ultrasensitive and quantification of SARS-CoV-2/N-Pro in humans and pets within 5 min (the LOQ as low as 75 fg/mL). The specificity, accuracy, stability, and actual blind sample tests show that the NG-IDME immunosensor is suitable for the detection of SARS-CoV-2 in humans and animals. This approach assists in monitoring the transmission of SARS-CoV-2-infected animals to humans.

Performance of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Targeting the RNA Polymerase Gene for the Direct Detection of SARS-CoV2 in Nasopharyngeal Swabs

In 2020, a global pandemic caused by SARS-CoV-2 was declared. Different institutes proposed diagnostic molecular methods to detect the virus in clinical samples. This study aims to validate and standardize the use of a loop-mediated isothermal amplification (LAMP)-based methodology targeting the viral RP gene, as a faster and low-cost diagnostic method for SARS-CoV-2 infections. The results obtained with RT-LAMP (Reverse Transcriptase) were compared to the results of real-time polymerase chain reaction (RT-PCR) to assess its sensitivity and specificity. In total, 115 samples (nasopharyngeal samples) were used for detecting SARS-CoV-2 by RT-LAMP, with 43 positives and 72 negatives. The study showed a positive predictive value (PPV) of 90.7% and a negative predictive value (VPN) of 100%. The LAMP assay also demonstrated a high sensitivity of 90.7% and a specificity of 100% (confidence interval 77.9-97.4%) when using the lower detection limit of 40 copies/µL. The RT-LAMP described here has the potential to detect even the new variants of SARS-CoV-2, suggesting that it may not be significantly affected by gene mutations. The RT-LAMP targeting the RP viral region is faster and less expensive than other molecular approaches, making it an alternative for developing countries.

Intestinal Villi-Inspired Mathematically Base-Layer Engineered Microneedles (IMBEMs) for Effective Molecular Exchange during Biomarker Enrichment and Drug Deposition in Diversified Mucosa

The mucosa-interfacing systems based on bioinspired engineering design for sampling/drug delivery have manifested crucial potential for the monitoring of infectious diseases and the treatment of mucosa-related diseases. However, their efficiency and validity are severely restricted by limited contact area for molecular transfer and dissatisfactory capture/detachment capability. Herein, inspired by the multilayer villus structure of the small intestine that enables high nutrient absorption, a trigonometric function-based periodic pattern was fabricated and integrated on the base layer of the microneedle patch, exhibiting a desirable synergistic effect with needle tips for deep sample enrichment and promising molecular transfer, significantly improving the device-mucosa bidirectional interaction. Moreover, mathematical modeling and finite element analysis were adopted to visualize and quantify the microcosmic molecular transmission process, guiding parameter optimization in actual situation. Encouragingly, these intestinal villi-inspired mathematically base-layer engineered microneedles (IMBEMs) have demonstrated distinguished applicability among mucosa tissue with varying surface curvatures, tissue toughness, and local environments, and simultaneously, have gained favorable support from healthy volunteers receiving preliminary test of IMBEMs patches. Overall, validated by numerous in vitro and in vivo tests, the IMBEMs were confirmed to act as a promising candidate to facilitate mucosa-based sampling and topical drug delivery, indicating highly clinical translation potential.

A comprehensive overview on the transmission, pathogenesis, diagnosis, treatment, and prevention of SARS-CoV-2

Severe acute respiratory syndrome coronavirus (SARS-CoV) is a single positive-strand RNA virus that is responsible for the current pandemic that the world has been facing since 2019. The primary route of transmission of SARS-CoV-2 is through respiratory tract transmission. However, other transmission routes such as fecal-oral, vertical transmission, and aerosol-eye also exist. In addition, it has been found that the pathogenesis of this virus involves the binding of the virus's S protein to its host cell surface receptor angiotensin-converting enzyme 2, which results in the subsequent membrane fusion that is required for SARS-CoV-2 to replicate and complete its entire life. The clinical symptoms of patients infected with SARS-CoV-2 can range from asymptomatic to severe. The most common symptoms seen include fever, dry cough, and fatigue. Once these symptoms are observed, a nucleic acid test is done using reverse transcription-polymerase chain reaction. This currently serves as the main confirmatory tool for COVID-19. Despite the fact that no cure has been found for SARS-CoV-2, prevention methods such as vaccines, specific facial mask, and social distancing have proven to be quite effective. It is imperative to have a complete understanding of the transmission and pathogenesis of this virus. To effectively develop new drugs as well as diagnostic tools, more knowledge about this virus would be needed.

Validation of N Protein Antibodies to Diagnose Previous SARS-CoV-2 Infection in a Large Cohort of Healthcare Workers: Use of Roche Elecsys® Immunoassay in the S Protein Vaccination Era

The aim of this study was to validate the detection of anti-nucleocapsid protein (N protein) antibodies for the diagnosis of SARS-CoV-2 infection in light of the fact that most COVID-19 vaccines use the spike (S) protein as the antigen. Here, 3550 healthcare workers (HCWs) were enrolled from May 2020 (when no S protein vaccines were available). We defined SARS-CoV-2 infection if HCWs were found to be positive by RT-PCR or found to be positive in at least two different serological immunoassays. Serum samples from Biobanc I3PT-CERCA were analyzed by Roche Elecsys^® (N protein) and Vircell IgG (N and S proteins) immunoassays. Discordant samples were reanalyzed with other commercial immunoassays. Roche Elecsys^® showed the positivity of 539 (15.2%) HCWs, 664 (18.7%) were found to be positive by Vircell IgG immunoassays, and 164 samples (4.6%) showed discrepant results. According to our SARS-CoV-2 infection criteria, 563 HCWs had SARS-CoV-2 infection. The Roche Elecsys^® immunoassay has a sensitivity, specificity, accuracy, and concordance with the presence of infection of 94.7%, 99.8%, 99.3%, and 0.96, respectively. Similar results were observed in a validation cohort of vaccinated HCWs. We conclude that the Roche Elecsys^® SARS-CoV-2 N protein immunoassay demonstrated good performance in diagnosing previous SARS-CoV-2 infection in a large cohort of HCWs.

Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection

Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. Cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure.

Asymptomatic and Mild SARS-CoV-2 Infections in a Hungarian Outpatient Cohort in the First Year of the COVID-19 Pandemic

We aimed to estimate the proportion of the population infected with SARS-CoV-2 in the first year of the pandemic. The study population consisted of outpatient adults with mild or no COVID-19 symptoms and was divided into subpopulations with different levels of exposure. Among the subpopulation without known previous COVID-19 contacts, 4143 patients were investigated. Of the subpopulation with known COVID-19 contacts, 594 patients were investigated. IgG- and IgA-seroprevalence and RT-PCR positivity were determined in context with COVID-19 symptoms. Our results suggested no significant age-related differences between participants for IgG positivity but indicated that COVID-19 symptoms occurred most frequently in people aged between 20 and 29 years. Depending on the study population, 23.4-74.0% PCR-positive people (who were symptomless SARS-CoV-2 carriers at the time of the investigation) were identified. It was also observed that 72.7% of the patients remained seronegative for 30 days or more after their first PCR-positive results. This study hoped to contribute to the scientific understanding of the significance of asymptomatic and mild infections in the long persistence of the pandemic.

A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field

Background

: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings.

Objectives

: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries.

Study design

: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 minutes. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied.

Results

: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay).

Conclusion

: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

An integrated dual-layer microfluidic platform for multiple respiratory viruses screening

Currently, the coronavirus disease 2019 (COVID-19) caused by the outbreak of a novel coronavirus (SARS-CoV-2) is spreading rapidly worldwide. Due to the high incidence of influenza coinciding with SARS-CoV-2, rapid detection is crucial to prevent spreading. Here, we present an integrated dual-layer microfluidic platform for specific and highly sensitive SARS-CoV-2, influenza viruses A (FluA) H1N1, H3N2, and influenza virus B (FluB) simultaneous detection. The platform includes a dual microchip (Dμchip) and a portable detection device for real-time fluorescence detection, temperature control and online communication. The Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) and Cas12a cleavage were performed on the Dμchip. The limit of detection (LoD) of the Dμchip assay was 10 copies for SARS-CoV-2, FluA H1N1, H3N2, and FluB RNAs. The Dμchip assay yielded no cross-reactivity against other coronaviruses, so it was suitable for the screening of multiple viruses. Moreover, the positive percentage agreement (PPA) and negative percentage agreement (NPA) of the assay were 97.9% and 100%, respectively, in 75 clinical samples compared to data from RT-PCR-based assays. Furthermore, the assay allowed the detection SARS-CoV-2 and influenza viruses in spiked samples. Overall, the present platform would provide a rapid method for the screening of multiple viruses in hospital emergency, community and primary care settings and facilitate the remote diagnosis and outbreak control of the COVID-19.

Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens

As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, p = 0.0507; copy number, p = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.

Modelling the epidemiological implications for SARS-CoV-2 of Christmas household bubbles in England

The emergence of SARS-CoV-2 saw severe detriments to public health being inflicted by COVID-19 disease throughout 2020. In the lead up to Christmas 2020, the UK Government sought an easement of social restrictions that would permit spending time with others over the Christmas period, whilst limiting the risk of spreading SARS-CoV-2. In November 2020, plans were published to allow individuals to socialise within 'Christmas bubbles' with friends and family. This policy involved a planned easing of restrictions in England between 23-27 December 2020, with Christmas bubbles allowing people from up to three households to meet throughout the holiday period. We estimated the epidemiological impact of both this and alternative bubble strategies that allowed extending contacts beyond the immediate household. We used a stochastic individual-based model for a synthetic population of 100,000 households, with demographic and SARS-CoV-2 epidemiological characteristics comparable to England as of November 2020. We evaluated five Christmas bubble scenarios for the period 23-27 December 2020, assuming our populations of households did not have symptomatic infection present and were not in isolation as the eased social restrictions began. Assessment comprised incidence and cumulative infection metrics. We tested the sensitivity of the results to a situation where it was possible for households to be in isolation at the beginning of the Christmas bubble period and also when there was lower adherence to testing, contact tracing and isolation interventions. We found that visiting family and friends over the holiday period for a shorter duration and in smaller groups was less risky than spending the entire five days together. The increases in infection from greater amounts of social mixing disproportionately impacted the eldest. We provide this account as an illustration of a real-time contribution of modelling insights to a scientific advisory group, the Scientific Pandemic Influenza Group on Modelling, Operational sub-group (SPI-M-O) for the Scientific Advisory Group for Emergencies (SAGE) in the UK, during the COVID-19 pandemic. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".

Similar Sensitivity of SARS-CoV-2 Detection in Oropharyngeal/Nasopharyngeal and Saliva Samples on the Hologic Panther Platform

BACKGROUND

Oropharyngeal (OP) and nasopharyngeal (NP) sampling has historically been considered the reference specimen type used for respiratory virus detection. Saliva could be a less invasive alternative for SARS-CoV-2 detection, but limited evidence is available.

METHODS

The technical and clinical performance of saliva was compared to OP/NP on the Hologic Panther platform with two Aptima assays, the End-Point Transcription-Mediated Amplification assay (EP-TMA) and Real-Time Transcription-Mediated Amplification assay (RT-TMA). The samples were collected at the Public Health Service Testing Site XL location in Schiphol Amsterdam Airport. At the site, the Regional Public Health Laboratory Kennemerland (RPHLK) has a fully equipped laboratory facility.

RESULTS

A total of 374 samples (187 OP/NP swabs and 187 saliva samples) were collected from 187 unique patients. The Real-Time Transcription-Mediated Amplification assay (RT-TMA) resulted in comparable sensitivities for the detection of SARS-CoV-2 in both the OP/NP swabs (88.3%; 113/128) and saliva samples (87.5%; 112/128). The End-Point Transcription-Mediated Amplification assay (EP-TMA) analyses showed a similar sensitivity (86.7%; 111/128) in the OP/NP swabs but a lower sensitivity in the saliva samples (80.5%; 103/128). Within the discordant analyses, we found no associations in the symptoms, earlier SARS-CoV-2 infections and eating, smoking, drinking and tooth brushing habits within one hour before testing.

CONCLUSIONS

The Hologic Panther platform Real-Time Transcription-Mediated Amplification assay (RT-TMA) yields a sensitivity for the detection of SARS-CoV-2 in saliva that is comparable to the OP/NP swabs derived from participants presenting themselves at a public health testing facility with minimal or mild symptoms.

Single-walled carbon nanotubes-based RNA protection and extraction improves RT-qPCR sensitivity for SARS-CoV-2 detection

The false-negative result of nucleic acid testing is an important cause of continued spread of COVID-19, while SARS-CoV-2 RNA degradation during transportation and nucleic acid extraction can lead to false-negative results. Here, we investigated that single-walled carbon nanotubes (SCNTs) could protect RNA from degradation for at least 4 days at room temperature. By constructing magnetism-functionalized SCNTs (MSCNTs), we developed a method that enabled protection and simple extraction of SARS-CoV-2 RNA, and the RNA-bound MSCNTs can be directly used for reverse transcription polymerase chain reaction (RT-qPCR) detection. The experimental results showed that 1 μg of MSCNTs adsorbed up to 24 ng of RNA. Notably, the MSCNTs-based method for extracting SARS-CoV-2 RNA from simulated nasopharyngeal swabs and saliva samples with mean recovery rates of 103% and 106% improved the sensitivity of RT-qPCR detection by 8-32 fold in comparison to current common methods. This improvement was largely attributable to the protection of RNA, enabling increased RNA load for downstream assays.

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

Background

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

Main body

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

Conclusion

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

Graphic Abstract

Electrochemical biosensors based on saliva electrolytes for rapid detection and diagnosis

In recent years, electrochemical biosensors (ECBSs) have shown significant potential for real-time disease diagnosis and in situ physical condition monitoring. As a multi-constituent oral fluid comprising various disease signaling biomarkers, saliva has drawn much attention in the field of point-of-care (POC) testing. In particular, during the outbreak of the COVID-19 pandemic, ECBSs which hold the simplicity of a single-step assay compared with the multi-step assay of traditional testing methods are expected to relieve the human and economic burden caused by the massive and long-term sample testing process. Noteworthily, ECBSs for the detection of SARS-CoV-2 in saliva have already been developed and may replace current testing methods. Furthermore, the detection scope has expanded from routine indices such as sugar and uric acid to abnormal biomarkers for early-stage disease detection and drug level monitoring, which further facilitated the evolution of ECBSs in the last 5 years. This review is divided into several main sections. First, we discussed the latest advancements and representative research on ECBSs for saliva testing. Then, we focused on a novel kind of ECBS, organic electrochemical transistors (OECTs), which hold great advantages of high sensitivity and signal-to-noise ratio and on-site detection. Finally, application of ECBSs with integrated portable platforms in oral cavities, which lead to powerful auxiliary testing means for telemedicine, has also been discussed.

Wastewater to clinical case (WC) ratio of COVID-19 identifies insufficient clinical testing, onset of new variants of concern and population immunity in urban communities

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-depth analysis and understanding of the metrics derived from WWS is required to interpret and utilize WWS-acquired data effectively (McClary-Gutierrez et al., 2021; O'Keeffe, 2021). In this study, the SARS-CoV-2 wastewater signal to clinical cases (WC) ratio was investigated across seven cities in Canada over periods ranging from 8 to 21 months. This work demonstrates that significant increases in the WC ratio occurred when clinical testing eligibility was modified to appointment-only testing, identifying a period of insufficient clinical testing (resulting in a reduction to testing access and a reduction in the number of daily tests) in these communities, despite increases in the wastewater signal. Furthermore, the WC ratio decreased significantly in 6 of the 7 studied locations, serving as a potential signal of the emergence of the Alpha variant of concern (VOC) in a relatively non-immunized community (40-60 % allelic proportion), while a more muted decrease in the WC ratio signaled the emergence of the Delta VOC in a relatively well-immunized community (40-60 % allelic proportion). Finally, a significant decrease in the WC ratio signaled the emergence of the Omicron VOC, likely because of the variant's greater effectiveness at evading immunity, leading to a significant number of new reported clinical cases, even when community immunity was high. The WC ratio, used as an additional monitoring metric, could complement clinical case counts and wastewater signals as individual metrics in its potential ability to identify important epidemiological occurrences, adding value to WWS as a diagnostic technology during the COVID-19 pandemic and likely for future pandemics.

Detection of SARS-CoV-2 Virus by Triplex Enhanced Nucleic Acid Detection Assay (TENADA)

SARS-CoV-2, a positive-strand RNA virus has caused devastating effects. The standard method for COVID diagnosis is based on polymerase chain reaction (PCR). The method needs expensive reagents and equipment and well-trained personnel and takes a few hours to be completed. The search for faster solutions has led to the development of immunological assays based on antibodies that recognize the viral proteins that are faster and do not require any special equipment. Here, we explore an innovative analytical approach based on the sandwich oligonucleotide hybridization which can be adapted to several biosensing devices including thermal lateral flow and electrochemical devices, as well as fluorescent microarrays. Polypurine reverse-Hoogsteen hairpins (PPRHs) oligonucleotides that form high-affinity triplexes with the polypyrimidine target sequences are used for the efficient capture of the viral genome. Then, a second labeled oligonucleotide is used to detect the formation of a trimolecular complex in a similar way to antigen tests. The reached limit of detection is around 0.01 nM (a few femtomoles) without the use of any amplification steps. The triplex enhanced nucleic acid detection assay (TENADA) can be readily adapted for the detection of any pathogen requiring only the knowledge of the pathogen genome sequence.

Advances in rapid detection of SARS-CoV-2 by mass spectrometry

COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.

Detection of A and B Influenza Viruses by Surface-Enhanced Raman Scattering Spectroscopy and Machine Learning

We demonstrate the possibility of applying surface-enhanced Raman spectroscopy (SERS) combined with machine learning technology to detect and differentiate influenza type A and B viruses in a buffer environment. The SERS spectra of the influenza viruses do not possess specific peaks that allow for their straight classification and detection. Machine learning technologies (particularly, the support vector machine method) enabled the differentiation of samples containing influenza A and B viruses using SERS with an accuracy of 93% at a concentration of 200 μg/mL. The minimum detectable concentration of the virus in the sample using the proposed approach was ~0.05 μg/mL of protein (according to the Lowry protein assay), and the detection accuracy of a sample with this pathogen concentration was 84%.

A brief review on the validation of biology methods for COVID-19 detection

The COVID-19 global pandemic has been going on for more than two years, and the evolution of SARS-CoV-2 with many variants of concern still poses a risk to public health. Sufficient access to qualified and validated testing plays an important role in detecting and alerting trends of the pandemic and provides evidence for making decisions in preventive strategies and policies. Depending on the method of testing and laboratory conditions, validation parameters (i.e., analytical sensitivity, limit of detection, diagnostic sensitivity, analytical specificity, diagnostic specificity, repeatability, reproducibility, robustness, positive predictive value, negative predictive value, applicability, practicability, and time to results) can be very different. With three main types of COVID-19 detection kits available, comprising nucleic acid, serological, and antigen detection, the kind of validation parameters that should be used becomes a complicated consideration and takes time to assess. Our review provides valuable and comprehensive information for laboratories in the assessment and selection of the optimal parameters to validate new COVID-19 test kits.

Challenges in the Differential Diagnosis of COVID-19 Pneumonia: A Pictorial Review

COVID-19 pneumonia represents a maximum medical challenge due to the virus's high contagiousness, morbidity, and mortality and the still limited possibilities of the health systems. The literature has primarily focused on the diagnosis, clinical-radiological aspects of COVID-19 pneumonia, and the most common possible differential diagnoses. Still, few studies have investigated the rare differential diagnoses of COVID-19 pneumonia or its overlap with other pre-existing lung pathologies. This article presents the main radiological features of COVID-19 pneumonia and the most common alternative diagnoses to establish the vital radiological criteria for a differential diagnosis between COVID-19 pneumonia and other lung pathologies with similar imaging appearance. The differential diagnosis of COVID-19 pneumonia is challenging because there may be standard radiologic features such as ground-glass opacities, crazy paving patterns, and consolidations. A multidisciplinary approach is crucial to define a correct final diagnosis, as an overlap of COVID-19 pneumonia with pre-existing lung diseases is often possible and suggests possible differential diagnoses. An optimal evaluation of HRTC can help limit the clinical evolution of the disease, promote therapy for patients and ensure an efficient allocation of human and economic resources.

Frequent mandatory COVID-19 testing may increase risky behavior

Mandatory surveillance testing programs are popular policies aimed to control SARS-CoV-2 and may be considered for future epidemics. However, if people believe that testing lowers their risk of infection, such policies could increase risky behavior and may even cause increased pathogen spread. Using data from two US universities, we find that frequent mandatory testing is associated with greater participation in events linked to COVID-19 spread. Women seem to be driving this association, and mediation analyses suggest this is partly due to women's higher perception of COVID-related health risks. Our results show the potential for adverse effects from epidemic control policies, both on average and across population subgroups. Undertaking mitigation measures to reduce such unintended consequences may therefore be important.

Rhinovirus as the main co-circulating virus during the COVID-19 pandemic in children

OBJECTIVE

Changes in the epidemiology of respiratory infections during the restrictions imposed as a response to the coronavirus disease 2019 (COVID-19) pandemic have been reported elsewhere. The present study's aim was to describe the prevalence of a large array of respiratory pathogens in symptomatic children and adolescents during the pandemic in Southern Brazil.

METHODS

Hospitalized and outpatients aged 2 months to 18 years with signs and symptoms of acute COVID-19 were prospectively enrolled in the study from May to November 2020 in two hospitals in a large metropolitan area in a Brazilian city. All participants performed a real-time PCR panel assessing 20 respiratory pathogens (three bacteria and 17 viruses).

RESULTS

436 participants were included, with 45 of these hospitalized. Rhinovirus was the most prevalent pathogen (216/436) followed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 97/436), with a coinfection of these two viruses occurring in 31/436 participants. The remaining pathogens were found in 24 symptomatic participants (adenovirus, n = 6; Chlamydophila pneumoniae, n = 1; coronavirus NL63, n = 2; human enterovirus, n = 7; human metapneumovirus, n = 2; Mycoplasma pneumoniae, n = 6). Hospitalization was more common among infants (p = 0.004) and those with pathogens other than SARS-CoV-2 (p = 0.001).

CONCLUSION

During the period of social distancing in response to COVID-19, the prevalence of most respiratory pathogens was unusually low. Rhinovirus remained as the main virus co-circulating with SARS-CoV-2. COVID-19 in symptomatic children was less associated with hospitalization than with other respiratory infections in children and adolescents.

Performance Evaluation of Developed Bangasure™ Multiplex rRT-PCR Assay for SARS-CoV-2 Detection in Bangladesh: A Blinded Observational Study at Two Different Sites

In this study, we evaluated the performance of the in-house developed rRT-PCR assay for SARS-CoV-2 RNA targeting the envelope (E) and nucleocapsid (N) genes with internal control as human RNase P. A total of 50 positive samples and 50 negative samples of SARS-CoV-2 were tested by a reference kit at site 1 and a subset (30 positives and 16 negatives) of these samples are tested blindly at site 2. The limit of detection (LoD) was calculated by using a replication-deficient complete SARS-CoV-2 genome and known copy numbers, where Pseudo-virus samples were used to evaluate accuracy. On site 1, among the 50 SARS-CoV-2 positive samples 24, 18, and eight samples showed high (Ct < 26), moderate (26 < Ct ≤ 32), and low (32 < Ct ≤ 38) viral load, respectively, whereas in site 2, out of 30 SARS-CoV-2 positive samples, high, moderate, and low viral loads were found in each of the 10 samples. However, SARS-CoV-2 was not detected in the negative sample. So, in-house assays at both sites showed 100% sensitivity and specificity with no difference observed between RT PCR machines. The Ct values of the in-house kit had a very good correlation with the reference kits. LoD was determined as 100 copies/mL. It also displayed 100% accuracy in mutant and wild-type SARS-CoV-2 virus. This Bangasure™ RT-PCR kit shows excellent performance in detecting SARS-CoV-2 viral RNA compared to commercially imported CE-IVD marked FDA authorized kits.

SARS-CoV-2 RNA Testing Using Different Assays—Impact on Testing Strategies in a Clinical Setting

In order to assess SARS-CoV-2 real time quantitative polymerase chain reaction (RT-qPCR) results in a real-life setting, three independent laboratories in Graz (Austria) set up a continuous cross comparison schedule. The following test systems were used: The QIAGEN NeuMoDx SARS-CoV-2 Assay, the Allplex™ 2019-nCoV Assay (Seegene) on a MicroLab Nimbus (Hamilton) platform combined with RealStar SARS-CoV-2 RT-PCR Assay (Altona Diagnostics GmbH), and the cobas SARS-CoV-2 test on a fully automated cobas 6800 system (Roche). A total of 200 samples were analysed, 184 (92%) were found to be concordant with all testing platforms, 14 (7%) discordant. Two (1%) samples tested invalid on a single platform and were excluded from further analysis. Discordant results were distributed randomly across the assays. The Ct values from all assays correlated closely with each other. All discordant samples showed Ct values ≥ 26. SARS-CoV-2 RT-qPCR assays may show considerable variability, especially in samples with low viral RNA concentrations. Decision makers should thus balance the advantages and disadvantages of RT-qPCR for mass screening and adopt suitable strategies that ensure a rational management of positive samples with high Ct values.

Prioritizing interventions for preventing COVID-19 outbreaks in military basic training

Like other congregate living settings, military basic training has been subject to outbreaks of COVID-19. We sought to identify improved strategies for preventing outbreaks in this setting using an agent-based model of a hypothetical cohort of trainees on a U.S. Army post. Our analysis revealed unique aspects of basic training that require customized approaches to outbreak prevention, which draws attention to the possibility that customized approaches may be necessary in other settings, too. In particular, we showed that introductions by trainers and support staff may be a major vulnerability, given that those individuals remain at risk of community exposure throughout the training period. We also found that increased testing of trainees upon arrival could actually increase the risk of outbreaks, given the potential for false-positive test results to lead to susceptible individuals becoming infected in group isolation and seeding outbreaks in training units upon release. Until an effective transmission-blocking vaccine is adopted at high coverage by individuals involved with basic training, need will persist for non-pharmaceutical interventions to prevent outbreaks in military basic training. Ongoing uncertainties about virus variants and breakthrough infections necessitate continued vigilance in this setting, even as vaccination coverage increases.

Sensitivity and Diagnostic Yield of the First SARS-CoV-2 Nucleic Acid Amplification Test Performed for Patients Presenting to the Hospital

IMPORTANCE

Early and accurate diagnostic testing for SARS-CoV-2 is essential to initiate appropriate treatment and infection control and prevention measures among patients presenting to the hospital.

OBJECTIVE

To evaluate the diagnostic sensitivity of the SARS-CoV-2 nucleic acid amplification test (NAAT) performed within 24 hours of arrival to the emergency department among a nationally representative sample of patients.

DESIGN, SETTING, AND PARTICIPANTS

This diagnostic study was conducted at 47 hospitals across 7 provinces in Canada participating in the Canadian COVID-19 Rapid Response Emergency Department Network among consecutive eligible patients presenting to a participating emergency department who were tested for SARS-CoV-2 from March 1, 2020, to December 31, 2021. Patients not tested within 24 hours of arrival and those presenting with a positive result from a test performed in the community were excluded.

MAIN OUTCOMES AND MEASURES

The primary outcome was a positive result from the SARS-CoV-2 NAAT. Outcome measures were the diagnostic sensitivity and yield of the SARS-CoV-2 NAAT.

RESULTS

Of 132 760 eligible patients (66 433 women [50.0%]; median age, 57 years [IQR, 37-74 years]), 17 174 (12.9%) tested positive for SARS-CoV-2 within 14 days of their first NAAT. The diagnostic sensitivity of the SARS-CoV-2 NAAT was 96.2% (17 070 of 17 740 [95% CI, 95.9%-96.4%]) among all of the tests performed. Estimates ranged from a high of 97.7% (1710 of 1751 [95% CI, 96.8%-98.3%]) on day 2 of symptoms to a low of 90.4% (170 of 188 [95% CI, 85.3%-94.2%]) on day 11 of symptoms among patients presenting with COVID-19 symptoms. Among patients reporting COVID-19 symptoms, the sensitivity of the SARS-CoV-2 NAAT was 97.1% (11 870 of 12 225 [95% CI, 96.7%-97.3%]) compared with 87.6% (812 of 927 [95% CI, 85.2%-89.6%]) among patients without COVID-19 symptoms. The diagnostic yield of the SARS-CoV-2 NAAT was 12.0% (18 985 of 158 004 [95% CI, 11.8%-12.2%]) and varied from a high of 20.0% (445 of 2229 [95% CI, 18.3%-21.6%]) among patients tested on day 10 after symptom onset to a low of 8.1% (1686 of 20 719 [95% CI, 7.7%-8.5%]) among patients presenting within the first 24 hours of symptom onset.

CONCLUSIONS AND RELEVANCE

This study suggests that the diagnostic sensitivity was high for the first SARS-CoV-2 NAAT performed in the hospital and did not vary significantly by symptom duration. Repeated testing of patients with negative test results should be avoided unless their pretest probability of disease is high.

Morphological and Phenotypic Characteristics of the Bovine Nasopharyngeal Mucosa and Associated Lymphoid Tissue

The mammalian nasopharynx is an anatomically complex region of the upper respiratory tract that directly communicates with the nasal cavity, laryngopharynx, oesophagus and trachea. The nasopharyngeal mucosa contains moderate quantities of mucosa-associated lymphoid tissue (MALT) that is appropriately located for immunological sampling but also creates vulnerability to pathogens. In recent years, the nasopharynx has been inculpated in the pathogenesis of important diseases of cattle (foot-and-mouth disease) and humans (COVID-19), yet the tissue has never been described in detail in any species. In order to characterize the morphology and cellular composition of the bovine nasopharynx, samples of mucosa were collected from the nasopharynx of five 8-13-month-old steers and examined using light microscopy, immunohistochemistry and multichannel immunofluorescence. Morphologically, the nasopharyngeal epithelium was highly heterogeneous, with a continuum ranging from stratified squamous epithelium to highly attenuated, follicle-associated epithelium (FAE). Distribution of MALT was similarly regionally variable ranging from absent to clusters of multiple lymphoid follicles. Phenotypic characterization demonstrated dense distributions of dendritic cells and T lymphocytes surrounding lymphoid follicles, which comprised mostly B lymphocytes. The FAE overlaying the lymphoid follicles also contained higher numbers of dendritic cells and lymphocytes compared with the adjacent non-lymphoid epithelium, although cytotoxic T cells were notably scarce in the FAE. The bovine nasopharyngeal lymphoid tissue had comparable elements to other MALTs with specific differences that may help to elucidate the pathogenesis of infectious agents that have specific tropism for this tissue.

SARS-CoV-2 transmission by asymptomatic healthcare workers positive to screening swab: an Italian study

BACKGROUND

SARS-CoV-2 spreads primarily through respiratory droplets of symptomatic individuals. With respect to asymptomatic individuals, there are conflicting results in the literature and a lack of studies specifically examining transmission in healthcare settings.

METHODS

The aim of this retrospective study, conducted in a northeastern Italian region, was to estimate the contagiousness of asymptomatic healthcare workers (HCWs) who tested positive for SARS-CoV-2. Asymptomatic HCWs who tested positive for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (rRT-PCR) at a regular screening nasopharyngeal or oropharyngeal swab between 1 February 2020 and 15 September 2020 were considered index cases. Contacts who were at high risk of infection and had follow-up swabs were included. Contacts were considered infected if they had a positive follow-up swab and/or symptoms associated with COVID-19 confirmed by a positive test within 14 days of exposure. Information was taken from records previously collected to identify contacts. Infectivity was estimated using the attack rate (AR) with a 95% confidence interval (95% CI).

RESULTS

Thirty-eight asymptomatic HCWs who were positive at the screening swab and 778 contacts were identified. Contacts included 63.8% of colleagues, 25.6% of patients, 7.7% of family members and 3.0% of other contacts. Seven contacts tested positive for SARS-CoV-2 (AR: 0.91%, 95% CI: 0.89-0.93). Five of them were family members (AR: 8.3%), one was a colleague (0.2%) and one was a contact of other type (4.2%).

CONCLUSIONS

Viral spread by asymptomatic HCWs was less than in other settings. Identification of risk factors for transmission and reliable indicators of infectivity would be important to prioritize preventive measures.

A feasibility study of COVID-19 detection using breath analysis by high-pressure photon ionization time-of-flight mass spectrometry

BACKGROUND

SARS-CoV-2 has caused a tremendous threat to global health. PCR and antigen testing have played a prominent role in the detection of SARS-CoV-2-infected individuals and disease control. An efficient, reliable detection tool is still urgently needed to halt the global COVID-19 pandemic. Recently, FDA emergency approved VOC as an alternative test for COVID-19 detection.

METHODS AND MATERIALS

In this case-control study, we prospectively and consecutively recruited 95 confirmed COVID-19 patients and 106 healthy controls in the designated hospital for treatment of COVID-19 patients in Shenzhen, China. Exhaled breath samples were collected and stored in customized bags and then detected by HPPI-TOFMS for volatile organic components (VOCs). Machine learning (ML) algorithms were employed for COVID-19 detection model construction. Participants were randomly assigned in a 5:2:3 ratio to the training, validation, and blinded test sets. The sensitivity (SEN), specificity (SPE), and other general metrics were employed for the VOCs based COVID-19 detection model performance evaluation.

RESULTS

The VOCs based COVID-19 detection model achieved good performance, with a SEN of 92.2% (95% CI: 83.8%, 95.6%), a SPE of 86.1% (95% CI: 74.8%, 97.4%) on blinded test set. Five potential VOC ions related to COVID-19 infection were discovered, which are significantly different between COVID-19 infected patients and controls.

CONCLUSIONS

This study evaluated a simple, fast, non-invasive VOCs-based COVID-19 detection method and demonstrated that it has good sensitivity and specificity in distinguishing COVID-19 infected patients from controls. It has great potential for fast and accurate COVID-19 detection.

Comparison of the Performance of 24 Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in the Diagnosis of Coronavirus Disease 2019 Patients

Background

The accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the key to control Coronavirus Disease-2019 (COVID-19). The performance of different antibody detection methods for diagnosis of COVID-19 is inconclusive.

Methods

Between 16 February and 28 February 2020, 384 confirmed COVID-19 patients and 142 healthy controls were recruited. 24 different serological tests, including 4 enzyme-linked immunosorbent assays (EIAs), 10 chemiluminescent immunoassays (CLIAs), and 10 lateral flow immunoassays (LFIAs), were simultaneously performed.

Results

The sensitivities of anti-SARS-CoV-2 IgG and IgM antibodies with different reagents ranged from 75 to 95.83% and 46.09 to 92.45%, respectively. The specificities of both anti-SARS-CoV-2 IgG and IgM were relatively high and comparable among different reagents, ranged from 88.03 to 100%. The area under the curves (AUCs) of different tests ranged from 0.733 to 0.984, and the AUCs of EIAs or CLIAs were significantly higher than those of LFIAs. The sensitivities of both IgG and IgM gradually increased with increase of onset time. After 3–4 weeks, the sensitivities of anti-SARS-CoV-2 IgG were maintained at a certain level but the sensitivities of IgM were gradually decreased. Six COVID-19 patients who displayed negative anti-SARS-CoV-2 results were associated with the factors such as older age, having underlying diseases, and using immunosuppressant.

Conclusion

Besides the purpose of assessing the impact of the SARS-CoV-2 pandemic in the population, SARS-CoV-2 antibody assays may have an adjunct role in the diagnosis and exclusion of COVID-19, especially by using high-throughput technologies (EIAs or CLIAs).

da Paixão Melo M, Ferreira da Silva M, de Jesus Gonçalves dos Santos N, de Souza Pessoa N, Silva de Araujo R, de Macedo Godim T, Fraga de Oliveira Tosta S, Brandão Nardy V, Cristina Faria E, Frederico de Carvalho Dominguez Souza B, Laís Almeida dos Santos J, Wikramaratna P, Giovanetti M, Alcântara LCJ, Lourenço J, Leal e Silva de Mello A. Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil

RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state's area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks.

Antibody Response to SARS-CoV-2 in the First Batch of COVID-19 Patients in China by a Self-Developed Rapid IgM-IgG Test

It has been over two years since the COVID-19 pandemic began and it is still an unprecedented global challenge. Here, we aim to characterize the antibody profile from a large batch of early COVID-19 cases in China, from January – March 2020. More than 1,000 serum samples from participants in Hubei and Zhejiang province were collected. A series of serum samples were also collected along the disease course from 70 patients in Shanghai and Chongqing for longitudinal analysis. The serologic assay (ALLtest) we developed was confirmed to have high sensitivity (92.58% - 97.55%) and high specificity (92.14% - 96.28%) for the detection of SARS-CoV-2 nucleocapsid-specific antibodies. Confirmed cases found in the Hubei Provincial Center for Disease Control and Prevention (HBCDC), showed a significantly (p = 0.0018) higher positive rate from the ALLtest than RNA test. Then, we further identified the disease course, age, sex, and symptoms that were correlating factors with our ALLtest results. In summary, we confirmed the high reliability of our ALLtest and its important role in COVID-19 diagnosis. The correlating factors we identified will require special attention during future clinical application.

Factors associated with mortality, length of hospital stay and diagnosis of COVID-19: Data from a field hospital

Background

During the pandemic of COVID-19, phylogenetic changes have been observed in the characteristics of the virus, in the diagnosis and treatment of the disease. The clinical course and the severe form of the disease depends on several factors. This study characterized the beginning setting for patient care of COVID-19 in a referral center in one of the main capital cities of Brazil. In addition, were evaluated the factors associated with mortality, length of stay, and diagnostic outcome.

Methods

A cross-sectional study was conducted during May 2020 (n = 1100). The association of the variables with outcome was evaluated by a multivariable logistic regression model, using odds ratios (OR) and 95 % confidence intervals (CI).

Results

Overall, 76 % of patients were COVID-19 positive, and 70 % were diagnosed by RT–qPCR. The majority were male (56 %), and over 52 years old (74 %), 68 % had hypertension, 44 % had diabetes mellitus, and 32 % were obese. The mean length of stay was 10 ± 8 days, which was higher in the 34 % who died (≥14; OR=2; 95 %CI=1.4–4) and who had hypertension (OR=2; 95 %CI=1.3–3) (P < 0.001). The mean length of stay was also higher (P = 0.008) for those patients with pulmonary impairment ≥ 50 % (10.72 ± 8.24), than those with< 50 % (8.98 ± 6.81). Age (>62 and 65 years) was associated with longer hospitalization (OR=2; 95 %CI=1.4–3) and death (OR=6; 95 %CI=3–11). The time of sample collection for RT–qPCR was different between positive and negative tests (P = 0.001), with the time of 4–10 days showing a greater chance for virus detection (OR=2.9; 95 %CI=1.6–5).

Conclusion

Death was associated with age and pulmonary impairment. The length of hospitalization was associated with age, hypertension, pulmonary impairment and death. The time of sample collection to perform RT–qPCR and the rapid test was associated with a positive result for COVID-19. These results highlight the ongoing challenge of diagnosing, treating, and mitigating the effects caused by the COVID-19 pandemic.

A Prospective Study of the Serological, Clinical, and Epidemiological Features of a SARS-CoV-2 Positive Pediatric Cohort

Background: SARS-CoV-2 was a global pandemic. Children develop a mild disease and may have a different rate of seroconversion compared to adults. The objective was to determine the number of seronegative patients in a pediatric cohort. We also reviewed the clinical−epidemiological features associated with seroconversion. Methods: A multicenter prospective observational study during September−November 2020, of COVID-19, confirmed by reverse transcription-polymerase chain reaction. Data were obtained 4−8 weeks after diagnosis. Blood samples were collected to investigate the humoral response, using three different serological methods. Results: A total of 111 patients were included (98 symptomatic), 8 were admitted to hospital, none required an Intensive Care Unit visit. Median age: 88 months (IQR: 24−149). Median time between diagnosis and serological test: 37 days (IQR: 34−44). A total of 19 patients were non-seroconverters when using three serological techniques (17.1%; 95% CI: 10.6−25.4); most were aged 2−10 years (35%, p < 0.05). Univariate analysis yielded a lower rate of seroconversion when COVID-19 confirmation was not present amongst household contacts (51.7%; p < 0.05). Conclusions: There was a high proportion of non-seroconverters. This is more commonly encountered in childhood than in adults. Most seronegative patients were in the group aged 2−10 years, and when COVID-19 was not documented in household contacts. Most developed a mild disease. Frequently, children were not the index case within the family.

Is COVID-19 mortality associated with test number?

Introduction

With the ongoing pandemic of coronavirus disease 2019 (COVID-19), there is an argument on whether we should increase the number of testing for the coronavirus (SARS-CoV-2) to mitigate the epidemic in a given country. Therefore, we investigated the correlation between testing number and mortality to evaluate the hypothesis.

Methods

Data on an open-access database of COVID-19 was retrieved. Member countries of the Organization for Economic Co-operation and Development (OECD), BRICs nations (Brazil, Russia, India, and China), and Taiwan were included in the analysis, but 2 countries were removed as outliers.

Results

There was a weak, positive correlation between mortality and testing (r = 0.34, P = 0.03). On regression analysis, there was a positive slope but the coefficient was very small (0.00064).

Conclusions

We found a very small positive correlation between testing number and mortality for COVID-19.