Circulation of SARS-CoV-2 Among Asylum Seekers: A Real-Life Experience to Address Health Equity in Piacenza, Italy

Aim of the Study: We aimed to evaluate the virus spreading among a migrant population previously excluded by community surveillance programs. Method(s): We conducted a retrospective study, collecting data about people without SARS-CoV-2-related symptoms who attended the outpatient clinic for undocumented migrants from November 1, 2020, to April 30, 2021. Patients who performed a nasopharyngeal swab and serologic test to evaluate the presence of antibody anti-SARS-CoV-2 were enrolled. Result(s): Overall, 240 people were included in our study. Of them, 15 (6.3%) were female, with a median age of 27.0 years (interquartile range [IQR], 24.3-32.1 years). Thirty-seven patients (15.4%) tested positive for SARS-CoV-2 at the nasopharyngeal swab during the study period. Of these, 16 had positive or low positive results for immunoglobulin G (IgG) and 3 tested positive for both IgG and IgM. Besides, 22 participants (9.2%) resulted positive to serological testing, but negative to polymerase chain reaction testing. The median age of SARS-CoV-2 positive patients (n = 59) was significantly higher than negative (29.6 [IQR, 25.0-35.0] vs 26.8 [IQR, 24.2-31.5], P = 0.022). Among positive patients, the most frequent nationality was Bangladeshi, with 24 people (40.7%, P < 0.001). The highest percentage of positive was found among the same nationality (51.1% of Bangladeshi tested positive). Conclusion(s): Our data underline the significantly higher prevalence of SARS-CoV-2 infection in the undocumented migrant population in respect of the general population of Piacenza province in the same period (15.4% vs 5.9%, P < 0.001). The extension of surveillance programs to the whole population, thus including undocumented people, is crucial to curb the spreading of the virus.Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.

The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is regarded as a threat because it spreads quickly across the world without requiring a passport or establishing an identity. This tiny virus has wreaked havoc on people's lives, killed people, and created psychological problems all over the world. The viral spike protein (S) significantly contributes to host cell entry, and mutations associated with it, particularly in the receptor-binding protein (RBD), either facilitate the escape of virus from neutralizing antibodies or enhance its transmission by increasing the affinity for cell entry receptor, angiotensin-converting enzyme 2 (ACE2). The initial variants identified in Brazil, South Africa, and the UK have spread to various countries. On the other hand, new variants are being detected in India and the USA. The viral genome and proteome were applied for molecular detection techniques, and nanotechnology particles and materials were utilized in protection and prevention strategies. Consequently, the SARS-CoV-2 pandemic has resulted in extraordinary scientific community efforts to develop detection methods, diagnosis tools, and effective antiviral drugs and vaccines, where prevailing academic, governmental, and industrial institutions and organizations continue to engage themselves in large-scale screening of existing drugs, both in vitro and in vivo. In addition, COVID-19 pointed on the possible solutions for the environmental pollution globe problem. Therefore, this review aims to address SARS-CoV-2, its transmission, where it can be found, why it is severe in some people, how it can be stopped, its diagnosis and detection techniques, and its relationship with the environment.

A Comparative Study of SARS, MERS with COVID-19

Background: B814, now's called Coronavirus first identified by Tyrrell and Bynoe in 1965 from the respiratory tract (embryonic tracheal) of an adult and later on during working on National Institutes of Health Robert Chanock used the term "OC" for same virus strain. After several years researchers reported that coronaviruses were caused disease in rats, mice, chickens, turkeys, calves, dogs, cats, rabbits etc. after effecting the enormous variety of animal, in year 2002-2003 it caused new respiratory disease named severe acute respiratory syndrome, (SARS) in southern China. Objective(s): The main objective of this article is to compare the status of various previous pandemics (i.e., SARS, MERS) with the current COVID-19 pandemic in terms of the life cycle, diagnosis process and prevention Results: On 31st December 2019, the World Health Organization (WHO) office in China received information regarding pneumonia cases of unknown etiology from the Wuhan district in central China. Subsequently, this new disease spread to China, and from there, to the rest of the world. By the end of March 2020, more than 2 million cases were confirmed of this new disease, with over 70000 deaths worldwide. After some time, researchers have identified that this new disease is caused by a novel beta-Coronavirus (virus SARS-CoV-2) and the new disease was named COVID-19. Since then, the Ministry of Health of various countries and WHO have been fighting this health emergency, which has not only affected public health, but also affected various economic sectors. Conclusion(s): The current outbreak SARS-CoV-2 phylogenetically resembled to Bat SARS, which was previously identified in year 2002 and 2012 having low mortality rate than MERS and SARS. However, SARS-CoV-2 and MERS having high virological similarity but both use different receptors to take entry in to the host cell via ACE-2 and DPP-4 respectively. Unfortunately, currently there is no approved treatment available worldwide. Currently, we can hope that together we will recover from this public health emergency very soon.Copyright © 2021 Bentham Science Publishers.

Correlation of Viral Load With the Biochemical and Hematological Profiles of COVID-19 Patients in Al Buraimi Hospital, Sultanate of Oman: A Cross-Sectional Study.

Background Rapid identification of COVID-19 is crucial during the pandemic for the treatment and management of patients. Thus, early diagnosis of the disease using laboratory parameters can help in the rapid management of infected patients. This study aimed to investigate the correlation of viral load with hematological and biochemical parameters. This will ultimately help physicians to better understand the dynamics of this novel virus and aid in the management of patients. Methodology Laboratory confirmation of SARS-CoV-2 was performed by reverse transcription-polymerase chain reaction (RT-PCR) at the Al-Buraimi Hospital Laboratory Department using oropharyngeal and nasopharyngeal swabs. Positive cases were collected from July 2020 to January 2021 to be enrolled in this study. Results In this study, 264 confirmed positive patients were included initially and divided into three groups according to their cycle threshold (Ct) values obtained by PCR. Out of the total 264 patients, 174 (65.9%) were male, while 90 (34.1%) were female. However, the final sample was only 253 patients who met the inclusion criteria. With regard to Ct values, the study population was divided into the following three groups: Group 1 with Ct values of 9-20 (n = 87; 34.4%), group 2 with Ct values of 21-30 (n = 122; 47.8%), and group 3 with Ct values of 31-42 (n = 44; 17.4%). Conclusions We found that the proportion of male patients infected with COVID-19 was higher compared to females. In addition, the highest incidence was among patients in the age group of 51-70 years. The ferritin and alanine transaminase levels were highest in the initial stage of the infection (group 1) and decreased at the recovery stage. However, neutrophil, lymphocyte, alkaline phosphatase, and C-reactive protein showed an increasing trend from high viral load groups to low viral load groups. The values of the rest of the parameters, such as albumin, total bilirubin, lactate dehydrogenase, and D-dimer, were slightly higher in the initial stage of the infection but the decreasing trend was low; therefore, they were not considered helpful in predicting the disease severity reflected by their Ct value in the three different groups.

Machine Learning Successfully Detects Patients with COVID-19 Prior to PCR Results and Predicts Their Survival Based on Standard Laboratory Parameters in an Observational Study.

INTRODUCTION: In the current COVID-19 pandemic, clinicians require a manageable set of decisive parameters that can be used to (i) rapidly identify SARS-CoV-2 positive patients, (ii) identify patients with a high risk of a fatal outcome on hospital admission, and (iii) recognize longitudinal warning signs of a possible fatal outcome. METHODS: This comparative study was performed in 515 patients in the Maria Sklodowska-Curie Specialty Voivodeship Hospital in Zgierz, Poland. The study groups comprised 314 patients with COVID-like symptoms who tested negative and 201 patients who tested positive for SARS-CoV-2 infection; of the latter, 72 patients with COVID-19 died and 129 were released from hospital. Data on which we trained several machine learning (ML) models included clinical findings on admission and during hospitalization, symptoms, epidemiological risk, and reported comorbidities and medications. RESULTS: We identified a set of eight on-admission parameters: white blood cells, antibody-synthesizing lymphocytes, ratios of basophils/lymphocytes, platelets/neutrophils, and monocytes/lymphocytes, procalcitonin, creatinine, and C-reactive protein. The medical decision tree built using these parameters differentiated between SARS-CoV-2 positive and negative patients with up to 90-100% accuracy. Patients with COVID-19 who on hospital admission were older, had higher procalcitonin, C-reactive protein, and troponin I levels together with lower hemoglobin and platelets/neutrophils ratio were found to be at highest risk of death from COVID-19. Furthermore, we identified longitudinal patterns in C-reactive protein, white blood cells, and D dimer that predicted the disease outcome. CONCLUSIONS: Our study provides sets of easily obtainable parameters that allow one to assess the status of a patient with SARS-CoV-2 infection, and the risk of a fatal disease outcome on hospital admission and during the course of the disease.

Comparison of Nasopharyngeal and Saliva Swab Nucleic Acid Amplification and Rapid Antigen Testing To Detect Omicron SARS-CoV-2 Variant of Concern: a Prospective Clinical Trial (OMICRON).

In November 2021, the World Health Organization declared the Omicron variant (B.1.1.519) a variant of concern. Since then, worries have been expressed regarding the ability of usual diagnostic tests to detect the Omicron variant. In addition, some recently published data suggested that the salivary reverse transcription (RT)-PCR might perform better than the current gold standard, nasopharyngeal (NP) RT-PCR. In this study, we aimed to compare the sensitivities of nasopharyngeal and saliva RT-PCR and assess the diagnostic performances of rapid antigen testing (RAT) in nasopharyngeal and saliva samples. We conducted a prospective clinical study among symptomatic health care professionals consulting the occupational health service of our hospital for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening and hospitalized patients in internal medicine/intensive care wards screened for SARS-CoV-2 with COVID-19-compatible symptoms. A composite outcome considering NP PCR and/or saliva PCR was used as a reference standard to define COVID-19 cases. A total of 475 paired NP/saliva specimens have been collected with a positivity rate of 40% (n = 192). NP and salivary RT-PCR exhibited sensitivities of 98% (95% CI, 94 to 99%) and 87% (95% CI, 81 to 91%), respectively, for outpatients (n = 453) and 94% (95% CI, 72 to 99%) and 69% (95% CI, 44 to 86%), respectively, for hospitalized patients (n = 22). Nasopharyngeal rapid antigen testing exhibited much lower diagnostic performances (sensitivity of 66% and 31% for outpatients and inpatients, respectively), while saliva RAT showed a sensitivity of less than 5% in both groups. Nasopharyngeal RT-PCR testing remains the gold standard for SARS-CoV-2 Omicron variant screening. Salivary RT-PCR can be used as an alternative in case of contraindication to perform NP sampling. The use of RAT should be limited to settings where access to molecular diagnostic methods is lacking. IMPORTANCE The Omicron variant of concern spread rapidly since it was first reported in November 2021 and currently accounts for the vast majority of new infections worldwide. Recent reports suggest that saliva sampling might outweigh nasopharyngeal sampling for the diagnosis of the Omicron variant. Nevertheless, data investigating the best diagnostic strategy specifically for the Omicron variant of concern remain scarce. This study fills this gap in current knowledge and elucidates the question of which strategy to use in which patient. It provides a new basis for further improving COVID-19 screening programs and managing patients suspected to have COVID-19.

SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic.

Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic service through the implementation of standardized protocols for biospecimen sampling, transportation, biobanking, preanalytical validation, and nucleic acids (NA) testing (NAT). Nasopharyngeal and oropharyngeal swabs collected in a special transportation medium were the biospecimens from which NAs were purified either manually or automatically. Viral RNA genome presence was determined using commercial SARS-CoV-2 detection kits (based on reverse transcription coupled with real-time PCR [RT-PCR]). Improvements in laboratory processing speed and reliability resulted from semi-automatizing laboratory processes and adopting a quality control/quality assurance system (QC/QA), respectively. NAs that were purified, either manually or automatically, were validated by preanalytical spectrophotometric characterization. Automated purification was less prone to contamination and reduced the processing time. The following six RT-PCR kits were evaluated for their convenience, specificity, sensitivity, time consumption, and required materials (in order, starting with the kit with the best results): RIDA gene and Viasure (tied), Vircell, LightMix, 1copy, and Logix Smart. Redesigning the laboratories' working areas, equipment, fluxes of personnel and material, and personnel skills, and overemphasizing biosafety safeguards were major challenges encountered in the middle of the sanitary crisis. Adopting a QC/QA system, utilizing automatization processes, and working closely with health authorities were key factors in our success. IMPORTANCE Rearranging our diagnostic laboratories to improve the fight against a new unexpected, unpredictable, and sudden public health threat demanded that we move quickly to redesign not only the laboratory processes but also the distribution of space, personnel activities, and fluxes of material coming in and out. We also had to work closely with governmental health authorities to gain their trust in our technical competence. Gaining the confidence of the clients, i.e., mainly individuals, the human resource departments of factories and corporations sending employees for testing, and medical institutions, and implementing as much automatization as possible of processes, in which only officially approved reagents (for extraction and analysis of NA) were used to generate opportune trustable testing results, were key factors. Our laboratories have gathered a considerable amount of experience and significant number of solutions, considering our geographic contexts alongside this continuously morphing pandemic, validating many techniques that might help other laboratories find a better and more precise workflow.

SARS-CoV-2 in a Mink Farm in Italy: Case Description, Molecular and Serological Diagnosis by Comparing Different Tests.

This study described a SARS-CoV-2 infection in minks on an Italian farm. Surveillance was performed based on clinical examination and a collection of 1879 swabs and 74 sera from dead and live animals. The farm was placed under surveillance for 4.5 months, from the end of July 2020, when a man working on the farm tested positive by RT-PCR, till mid-December 2020 when all the animals were sacrificed. Clinical examination revealed no clinical signs or increased mortality rates attributable to SARS-CoV-2, while diagnostic tests detected only four weak PCR-positive samples, but 100% of sera were positive for SARS-CoV-2 anti-S antibodies. The phylogenetic analysis of two SARS-CoV-2 sequences from two minks and the sequence of the worker showed that they belonged to different clades. It could be therefore assumed that two distinct introductions of the virus occurred on the farm, and that the first introduction probably occurred before the start of the surveillance period. From the data collected, and especially from the detection of specific antibodies through the combination of different tests, it can be postulated that syndromic surveillance combined with genome detection by PCR may not be sufficient to achieve a diagnosis in asymptomatic animals. In particular, the serological approach, especially when using tests directed towards the S protein, may be useful for improving the traceability of virus circulation in similar environments.

A Supervised Multi-tree XGBoost Model for an Earlier COVID-19 Diagnosis Based on Clinical Symptoms

Efficient screening of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) enables quick and efficient diagnosis of SARS-CoV-2 and can mitigate the burden on healthcare systems. The aim was to assist the medical team globally in triaging incoming patients, especially in countries with limited healthcare infrastructure. In this context, the features with imminent infection risk (Test Indication, Fever, and Headache) were obtained using a multi-tree XGBoost algorithm. Based on their feature importance, the top three clinically relevant earlier clinical symptoms (attributes) were employed to create a Multi-tree XGBoost-based model for an earlier prediction of SARS-CoV-2. Overall, our Multi-tree XGBoost model predicted SARS-CoV-2 infection status with a high F1-score (0.9920 +/- 0.008) and AUC value (0.9974 +/- 0.0026) only by assessing the primary three clinical symptoms related to COVID-19 infection. Thus our multi-tree XGBoost - based model suggests a simple and accurate method for earlier detection of SARS-CoV-2 cases and initiating proper treatment protocol for SARS-CoV-2 positive patients. Therefore, we can conclude that our model will allow the health organizations to potentially reduce the infection rate and mortality in masses with COVID-19 infection and fatality due to SARS-CoV-2.

Decrease in Angiotensin-Converting Enzyme activity but not concentration in plasma/lungs in COVID-19 patients offers clues for diagnosis/treatment.

Although several therapeutics are used to treat coronavirus disease 2019 (COVID-19) patients, there is still no definitive metabolic marker to evaluate disease severity and recovery or a quantitative test to end quarantine. Because severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects human cells via the angiotensin-converting-enzyme 2 (ACE2) receptor and COVID-19 is associated with renin-angiotensin system dysregulation, we evaluated soluble ACE2 (sACE2) activity in the plasma/saliva of 80 hospitalized COVID-19 patients and 27 non-COVID-19 volunteers, and levels of ACE2/Ang (1-7) in plasma or membrane (mACE2) in lung autopsy samples. sACE2 activity was markedly reduced (p < 0.0001) in COVID-19 plasma (n = 59) compared with controls (n = 27). Nadir sACE2 activity in early hospitalization was restored during disease recovery, irrespective of patient age, demographic variations, or comorbidity; in convalescent plasma-administered patients (n = 45), restoration was statistically higher than matched controls (n = 22, p = 0.0021). ACE2 activity was also substantially reduced in the saliva of COVID-19 patients compared with controls (p = 0.0065). There is a strong inverse correlation between sACE2 concentration and sACE2 activity and Ang (1-7) levels in participant plasmas. However, there were no difference in membrane ACE2 levels in lungs of autopsy tissues of COVID-19 (n = 800) versus other conditions (n = 300). These clinical observations suggest sACE2 activity as a potential biomarker and therapeutic target for COVID-19.

Factors associated with weak positive SARS-CoV-2 diagnosis by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR).

During the COVID-19 pandemic, the reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) assay has been the primary method of diagnosis of SARS-CoV-2 infection. However, RT-qPCR assay interpretation can be ambiguous with no universal absolute cut-off value to determine sample positivity, which particularly complicates the analysis of samples with high Ct values, or weak positives. Therefore, we sought to analyse factors associated with weak positive SARS-CoV-2 diagnosis. We analysed sample data associated with all positive SARS-CoV-2 RT-qPCR diagnostic tests performed by the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Melbourne, Australia, during the Victorian first wave (22 January 2020-30 May 2020). A subset of samples was screened for the presence of host DNA and RNA using qPCR assays for CCR5 and 18S, respectively. Assays targeting the viral RNA-dependent RNA polymerase (RdRp) had higher Ct values than assays targeting the viral N and E genes. Weak positives were not associated with the age or sex of individuals' samples nor with reduced levels of host DNA and RNA. We observed a relationship between Ct value and time post-SARS-CoV-2 diagnosis. High Ct value or weak positive SARS-CoV-2 was not associated with any particular bias including poor biological sampling.

B-Cell-Epitope-Based Fluorescent Quantum Dot Biosensors for SARS-CoV-2 Enable Highly Sensitive COVID-19 Antibody Detection.

A new antibody diagnostic assay with more rapid and robust properties is demanded to quantitatively evaluate anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity in a large population. Here, we developed a nanometer-scale fluorescent biosensor system consisting of CdSe-ZnS quantum dots (QDs) coupled with the highly sensitive B-cell epitopes of SARS-CoV-2 that could remarkably identify the corresponding antibody with a detection limit of 100 pM. Intriguingly, we found that fluorescence quenching of QDs was stimulated more obviously when coupled with peptides than the corresponding proteins, indicating that the energy transfer between QDs and peptides was more effective. Compared to the traditional enzyme-linked immunosorbent assay (ELISA), the B-cell-epitope-based QD-biosensor could robustly distinguish coronavirus disease 2019 (COVID-19) antibody-positive patients from uninfected individuals with a higher sensitivity (92.3-98.1% positive rates by QD-biosensor vs. 78.3-83.1% positive rates by ELISAs in 207 COVID-19 patients' sera) in a more rapid (5 min) and labor-saving manner. Taken together, the 'QD-peptides' biosensor provided a novel real-time, quantitative, and high-throughput method for clinical diagnosis and home-use tests.

Optimization of loop-mediated isothermal amplification (LAMP) assay for robust visualization in SARS-CoV-2 and emerging variants diagnosis.

Loop-mediated isothermal amplification (LAMP) is widely used in detection of pathogenic microorganisms including SARS-CoV-2. However, the performance of LAMP assay needs further exploration in the emerging SARS-CoV-2 variants test. Here, we design serials of primers and select an optimal set for LAMP-based on SARS-CoV-2 N gene for a robust and visual assay in SARS-CoV-2 diagnosis. The limit of detectable template reaches 10 copies of N gene per 25 µL reaction at isothermal 58℃ within 40 min. Importantly, the primers for LAMP assay locate at 12 to 213 nt of N gene, a highly conservative region, which serves as a compatible test in emerging SARS-CoV-2 variants. Comparison to a commercial qPCR assay, this LAMP assay exerts the high viability in diagnosis of 41 clinical samples. Our study optimizes an advantageous LAMP assay for colorimetric detection of SARS-CoV-2 and emerging variants, which is hopeful to be a promising test in COVID-19 surveillance.

Automatic system for high-throughput and high-sensitivity diagnosis of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had severe consequences for health and the global economy. To control the transmission, there is an urgent demand for early diagnosis and treatment in the general population. In the present study, an automatic system for SARS-CoV-2 diagnosis is designed and built to deliver high specification, high sensitivity, and high throughput with minimal workforce involvement. The system, set up with cross-priming amplification (CPA) rather than conventional reverse transcription-polymerase chain reaction (RT-PCR), was evaluated using more than 1000 real-world samples for direct comparison. This fully automated robotic system performed SARS-CoV-2 nucleic acid-based diagnosis with 192 samples in under 180 min at 100 copies per reaction in a "specimen in data out" manner. This throughput translates to a daily screening capacity of 800-1000 in an assembly-line manner with limited workforce involvement. The sensitivity of this device could be further improved using a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based assay, which opens the door to mixed samples, potentially include SARS-CoV-2 variants screening in extensively scaled testing for fighting COVID-19.

Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART).

Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.

Development and clinical evaluation of a rapid antibody lateral flow assay for the diagnosis of SARS-CoV-2 infection.

BACKGROUND: The novel coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has quickly spread worldwide since its outbreak in December 2019. One of the primary measures for controlling the spread of SARS-CoV-2 infection is an accurate assay for its diagnosis. SARS-CoV-2 real-time PCR kits suffer from some limitations, including false-negative results in the clinic. Therefore, there is an urgent need for the development of a rapid antibody test kit for COVID-19 diagnosis. METHODS: The nuclear capsid protein (N) and spike protein 1 (S1) fragments of SARS-CoV-2 were expressed in Escherichia coli, and rapid antibody-based tests for the diagnosis of SARS-CoV-2 infection were developed. To evaluate their clinical applications, the serum from COVID-19 patients, suspected COVID-19 patients, recovering COVID-19 patients, patients with general fever or pulmonary infection, doctors and nurses who worked at the fever clinic, and health professionals was analyzed by the rapid antibody test kits. The serum from patients infected with Mycoplasma pneumoniae and patients with respiratory tract infection was further analyzed to test its cross-reactivity with other respiratory pathogens. RESULTS: A 47 kDa N protein and 67 kDa S1 fragment of SARS-CoV-2 were successfully expressed, purified, and renatured. The rapid antibody test with recombinant N protein showed higher positive rate than the rapid IgM antibody test with recombinant S1 protein. Clinical evaluation showed that the rapid antibody test kit with recombinant N protein had 88.56 % analytical sensitivity and 97.42 % specificity for COVID-19 patients, 53.48 % positive rate for suspected COVID-19 patients, 57.14 % positive rate for recovering COVID-19 patients, and 0.5-0.8 % cross-reactivity with other respiratory pathogens. The analytical sensitivity of the kit did not significantly differ in COVID-19 patients with different disease courses (p < 0.01). CONCLUSIONS: The rapid antibody test kit with recombinant N protein has high specificity and analytical sensitivity, and can be used for the diagnosis of SARS-CoV-2 infection combined with RT-PCR.

Optimization and Standardization of Human Saliva Collection for MALDI-TOF MS.

SARS-CoV-2 outbreak led to unprecedented innovative scientific research to preclude the virus dissemination and limit its impact on life expectancy. Waiting for the collective immunity by vaccination, mass-testing, and isolation of positive cases remain essential. The development of a diagnosis method requiring a simple and non-invasive sampling with a quick and low-cost approach is on demand. We hypothesized that the combination of saliva specimens with MALDI-TOF MS profiling analyses could be the winning duo. Before characterizing MS saliva signatures associated with SARS-CoV-2 infection, optimization and standardization of sample collection, preparation and storage up to MS analyses appeared compulsory. In this view, successive experiments were performed on saliva from healthy healthcare workers. Specimen sampling with a roll cotton of Salivette® devices appeared the most appropriate collection mode. Saliva protein precipitation with organic buffers did not improved MS spectra profiles compared to a direct loading of samples mixed with acetonitrile/formic acid buffer onto MS plate. The assessment of sample storage conditions and duration revealed that saliva should be stored on ice until MS analysis, which should occur on the day of sampling. Kinetic collection of saliva highlighted reproducibility of saliva MS profiles over four successive days and also at two-week intervals. The intra-individual stability of saliva MS profiles should be a key factor in the future investigation for biomarkers associated with SARS-CoV-2 infection. However, the singularity of MS profiles between individuals will require the development of sophisticated bio-statistical analyses such as machine learning approaches. MALDI-TOF MS profiling of saliva could be a promising PCR-free tool for SARS-CoV-2 screening.

Interest of the cellular population data analysis as an aid in the early diagnosis of SARS-CoV-2 infection.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) is characterized by a high contagiousness requiring isolation measures. At this time, diagnosis is based on the positivity of specific RT-PCR and/or chest computed tomography scan, which are time-consuming and may delay diagnosis. Complete blood count (CBC) can potentially contribute to the diagnosis of COVID-19. We studied whether the analysis of cellular population data (CPD), provided as part of CBC-Diff analysis by the DxH 800 analyzers (Beckman Coulter), can help to identify SARS-CoV-2 infection. METHODS: Cellular population data of the different leukocyte subpopulations were analyzed in 137 controls, 322 patients with proven COVID-19 (COVID+), and 285 patients for whom investigations were negative for SARS-CoV-2 infection (COVID-). When CPD of COVID+ were different from controls and COVID- patients, we used receiver operating characteristic analysis to test the discriminating capacity of the individual parameters. Using a random forest classifier, we developed the algorithm based on the combination of 4 monocyte CPD to discriminate COVID+ from COVID- patients. This algorithm was tested prospectively in a series of 222 patients referred to the emergency unit. RESULTS: Among the 222 patients, 86 were diagnosed as COVID-19 and 60.5% were correctly identified using the discriminating protocol. Among the 136 COVID- patients, 10.3% were misclassified (specificity 89.7%, sensitivity 60.5%). False negatives were observed mainly in patients with a low inflammatory state whereas false positives were mainly seen in patients with sepsis. CONCLUSION: Consideration of CPD could constitute a first step and potentially aid in the early diagnosis of COVID-19.

Diagnostic testing for SARS-CoV-2 infection in HHT patients: nasopharyngeal versus oropharyngeal swab.

On March 11, 2020, WHO has defined the novel coronavirus disease SARS-CoV-2 (COVID-19) outbreak as a pandemic that still today continues to affect much of the world. Among the reasons for the rapid spread of SARS-CoV-2 infection, there is the role of asymptomatic or minimally symptomatic carriers. Therefore diagnostic testing is central to contain the global pandemic. Up to now real-time reverse transcriptase polymerase chain reaction-based molecular assays for detecting SARS-CoV-2 in respiratory specimens is the current reference standard for COVID-19 diagnosis. Based on current knowledge regarding the sensitivity of the molecular test, the highest positive detection rate is from lower respiratory tract specimens; alternatively it is possible to perform a nasopharyngeal or oropharyngeal swab. Nasopharyngeal swab is the preferred choice for SARS-CoV-2 testing since it seems to have a greater sensitivity; however the procedure is not always free of complications and an epistaxis can occur. Among patients with greatest risk of massive nosebleed there are HHT patients. Hereditary hemorrhagic telangiectasia is an autosomal dominant disease that leads to multiregional mucocutanous telangiectases and visceral arteriovenous malformations. Clinically, the presence of telangiectases in nasal mucosa is the cause of recurrent epistaxis. In HHT patients the execution of the nasopharyngeal swab can determine from little or no consequences to a massive epistaxis leading to the necessity of nasal packing generally followed by hospital admission. In HHT patients undergoing a diagnostic test to evaluate the SARS-CoV-2 infection status, especially in those patients with frequent epistaxis with a history of anemia and repeated hospitalizations, it is therefore advisable to perform an oropharyngeal swab. This, compared to the nasopharyngeal swab, exposes to a lower risk of severe nosebleeds related treatments, such as blood transfusions or invasive procedures. According to the risk-benefit assessment and based on our experience, we consider that, despite a lower diagnostic sensitivity, oropharyngeal swab is preferable to nasopharyngeal swab for the diagnosis of SARS CoV-2 infection in patients with HHT.