Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2

During virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.

Rapid Large-Scale COVID-19 Testing During Shortages

The Coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in economic and social lockdowns in most countries all over the globe. Early identification of infected individuals is regarded as one of the most important prerequisites for fighting the pandemic and for returning to a ‘New Normal’. Large-scale testing is therefore crucial, but is facing several challenges including shortage of sample collection tools and of molecular biological reagents, and the need for safe electronic communication of medical reports. We present the successful establishment of a holistic SARS-CoV-2 testing platform that covers proband registration, sample collection and shipment, sample testing, and report issuing. The RT-PCR-based virus detection, being central to the platform, was extensively validated: sensitivity and specificity were defined as 96.8% and 100%, respectively; intra-run and inter-run precision were <3%. A novel type of sample swab and an in-house-developed RNA extraction system were shown to perform as good as commercially available products. The resulting flexibility guarantees independence from the current bottlenecks in SARS-CoV-2 testing. Based on our technology, we offered testing at local, national, and global levels. In the present study, we report the results from approx. 18,000 SARS-CoV-2 tests in almost 10,000 individuals from a low-frequency SARS-CoV-2 pandemic area in a homogenous geographical region in north-eastern Germany for a period of 10 weeks (21 March to 31 May 2020). Among the probands, five SARS-CoV-2 positive cases were identified. Comparative analysis of corresponding virus genomes revealed a diverse origin from three of the five currently recognized SARS-CoV-2 phylogenetic clades. Our study exemplifies how preventive SARS-CoV-2 testing can be set up in a rapid and flexible manner. The application of our test has enabled a safe maintenance/resume of critical local infrastructure, e.g., nursing homes where more than 5000 elderlies and caretakers got tested. The strategy outlined by the present study may serve as a blueprint for the implementation of large-scale preventive SARS-CoV-2 testing elsewhere.

SARS-CoV-2 is transmitted via contact and via the air between ferrets

SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.

SARS-CoV-2 is transmitted via contact and via the air between ferrets

SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.

Presenting Features and Early Mortality from SARS-CoV-2 Infection in Cancer Patients during the Initial Stage of the COVID-19 Pandemic in Europe

We describe the outcomes in cancer patients during the initial outbreak of the COVID-19 in Europe from the retrospective, multi-center observational OnCovid study. We identified 204 cancer patients from eight centers in the United Kingdom, Italy, and Spain aged > 18 (mean = 69) and diagnosed with COVID-19 between February 26th and April 1st, 2020. A total of 127 (62%) were male, 184 (91%) had a diagnosis of solid malignancy, and 103 (51%) had non-metastatic disease. A total of 161 (79%) had > 1 co-morbidity. A total of 141 (69%) patients had > 1 COVID-19 complication. A total of 36 (19%) were escalated to high-dependency or intensive care. A total of 59 (29%) died, 53 (26%) were discharged, and 92 (45%) were in-hospital survivors. Mortality was higher in patients aged > 65 (36% versus 16%), in those with > 2 co-morbidities (40% versus 18%) and developing > 1 complication from COVID-19 (38% versus 4%, p = 0.004). Multi-variable analyses confirmed age > 65 and > 2 co-morbidities to predict for patient mortality independent of tumor stage, active malignancy, or anticancer therapy. During the early outbreak of SARS-CoV-2 infection in Europe co-morbid burden and advancing age predicted for adverse disease course in cancer patients. The ongoing OnCovid study will allow us to compare risks and outcomes in cancer patients between the initial and later stages of the COVID-19 pandemic.

Lack of sensitivity of an IVD/CE-labelled kit targeting the S gene for detection of SARS-CoV-2

OBJECTIVES

New molecular tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being rapidly launched in response to the coronavirus disease 2019 (COVID-19) pandemic. The aim of this study was to evaluate the analytical and clinical performance of the VIASURE SARS-CoV-2 S gene RT-PCR Kit on the BD Max™ system and to compare results with those obtained with the cobas® SARS-CoV-2 test on the cobas® 6800 system.

METHODS

For testing the analytical performance, reference material was used. Clinical samples (n = 101) obtained from individuals with symptoms compatible with COVID-19 were studied. Oropharyngeal and nasopharyngeal swabs were collected by using either ESwab™ or UTM™ collection systems.

RESULTS

When the analytical performance was evaluated, the sample containing the lowest SARS-CoV-2 concentration tested negative with the VIASURE test whereas results obtained with the cobas® test were found to be concordant with the results expected. Six out of the 101 clinical samples (5.9%) showed an inhibition with the VIASURE test. When analysing the remaining 95 clinical samples, 27 were found to be negative with both assays. Of 68 samples that were positive with the cobas® test, the VIASURE test missed 21 (30.9 %) samples. All of those 21 samples had shown Ct values ≥ 31 with the cobas® 6800 system. None of the samples tested positive with the VIASURE test and negative with the cobas® test.

CONCLUSIONS

The VIASURE test was impaired by a lack of sensitivity and a relatively high number of invalid results. When using the VIASURE test for routine testing, a significant number of COVID-19-positive samples would have been missed.

SARS-CoV-2 is transmitted via contact and via the air between ferrets

SARS-CoV-2, a coronavirus that emerged in late 2019, has spread rapidly worldwide, and information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets, 1 to 3 days and 3 to 7 days after exposure respectively. The pattern of virus shedding in the direct contact and indirect recipient ferrets is similar to that of the inoculated ferrets and infectious virus is isolated from all positive animals, showing that ferrets are productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings.

Longitudinal Change of Severe Acute Respiratory Syndrome Coronavirus 2 Antibodies in Patients with Coronavirus Disease 2019

BACKGROUND

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently emerged and caused the rapid spread of coronavirus disease 2019 (COVID-19) worldwide.

METHODS

We did a retrospective study and included COVID-19 patients admitted to Renmin Hospital of Wuhan University between 1 February and 29 February 2020. Antibody assay was conducted to detect COVID-19 envelope protein E and nucleocapsid protein N antigen.

RESULTS

One hundred twelve patients were recruited with symptoms of fever, cough, fatigue, myalgia, and diarrhea. All patients underwent antibody tests. Fifty-eight (51.79%) were positive for both immunoglobulin M (IgM) and immunoglobulin G (IgG), 7 (6.25%) were negative for both antibodies, 1 (0.89%) was positive for only IgM, and 46 (41.07%) were positive for only IgG. IgM antibody appeared within a week post-disease onset, lasted for 1 month, and gradually decreased, whereas IgG antibody was produced 10 days after infection and lasted for a longer time. However, no significant difference in levels of IgM and IgG antibodies between positive and negative patients of nucleic acid test after treatment was found.

CONCLUSIONS

Our results indicate that serological tests could be a powerful approach for the early diagnosis of COVID-19.

SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study

Background

In December, 2019, a novel zoonotic severe acute respiratory syndrome-related coronavirus emerged in China. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became pandemic within weeks and the number of human infections and severe cases is increasing. We aimed to investigate the susceptibilty of potential animal hosts and the risk of anthropozoonotic spill-over infections.

Methods

We intranasally inoculated nine fruit bats (Rousettus aegyptiacus), ferrets (Mustela putorius), pigs (Sus scrofa domesticus), and 17 chickens (Gallus gallus domesticus) with 10⁵ TCID₅₀ of a SARS-CoV-2 isolate per animal. Direct contact animals (n=3) were included 24 h after inoculation to test viral transmission. Animals were monitored for clinical signs and for virus shedding by nucleic acid extraction from nasal washes and rectal swabs (ferrets), oral swabs and pooled faeces samples (fruit bats), nasal and rectal swabs (pigs), or oropharyngeal and cloacal swabs (chickens) on days 2, 4, 8, 12, 16, and 21 after infection by quantitative RT-PCR (RT-qPCR). On days 4, 8, and 12, two inoculated animals (or three in the case of chickens) of each species were euthanised, and all remaining animals, including the contacts, were euthanised at day 21. All animals were subjected to autopsy and various tissues were collected for virus detection by RT-qPCR, histopathology immunohistochemistry, and in situ hybridisation. Presence of SARS-CoV-2 reactive antibodies was tested by indirect immunofluorescence assay and virus neutralisation test in samples collected before inoculation and at autopsy.

Findings

Pigs and chickens were not susceptible to SARS-CoV-2. All swabs, organ samples, and contact animals were negative for viral RNA, and none of the pigs or chickens seroconverted. Seven (78%) of nine fruit bats had a transient infection, with virus detectable by RT-qPCR, immunohistochemistry, and in situ hybridisation in the nasal cavity, associated with rhinitis. Viral RNA was also identified in the trachea, lung, and lung-associated lymphatic tissue in two animals euthanised at day 4. One of three contact bats became infected. More efficient virus replication but no clinical signs were observed in ferrets, with transmission to all three direct contact animals. Mild rhinitis was associated with viral antigen detection in the respiratory and olfactory epithelium. Prominent viral RNA loads of 0–10⁴ viral genome copies per mL were detected in the upper respiratory tract of fruit bats and ferrets, and both species developed SARS-CoV-2-reactive antibodies reaching neutralising titres of up to 1/1024 after 21 days.

Interpretation

Pigs and chickens could not be infected intranasally by SARS-CoV-2, whereas fruit bats showed characteristics of a reservoir host. Virus replication in ferrets resembled a subclinical human infection with efficient spread. Ferrets might serve as a useful model for further studies—eg, testing vaccines or antivirals.

Funding

German Federal Ministry of Food and Agriculture.

Impact of the Coronavirus Infection in Pregnancy: A Preliminary Study of 141 Patients

Background

The novel coronavirus disease (COVID-19) is the most challenging health crisis that we are facing today. Against the backdrop of this pandemic, it becomes imperative to study the effects of this infection on pregnancy and its outcome. Hence, the present study was undertaken to evaluate the effects of COVID-19 infection on the maternal morbidity and mortality, the course of labour as well as the neonatal outcome.

Materials and Methods

A total of 977 pregnant women were included in the study, from 1st April to 15th May 2020 at a tertiary care hospital. There were 141 women who tested COVID positive and remaining 836 patients were included in the COVID negative group. Findings were compared in both the groups.

Results

The incidence of COVID positive pregnant women was found to be 14.43%. More patients delivered by LSCS in the COVID positive and the COVID negative group (50%) as compared to COVID negative group (47%), (p > 0.05). Low APGAR score (0-3) was observed in 2(1.52%) neonates of COVID positive mothers and in 15 (1.91%) neonates of COVID negative mothers. Overall most of the babies were healthy. Out of all babies tested, 3 were detected positive initially which were retested on day 5 and were found to be negative.

Conclusion

There is no significant effect of COVID infection on maternal and foetal outcome in pregnancy and there is no evidence of vertical transmission of the COVID-19 infection but long-term follow-up of these babies is recommended.

An optimisation of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams

Background: The global COVID-19 outbreak relies on a quantitative real-time polymerase chain reaction (qRT-PCR) for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2), to facilitate the roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers' recommendations to sustain the testing capability in our setting, where the supply of testing reagents is limited. Methods: Standards generated from a serially-diluted positive control and previously identified positive/negative samples were used to determine the optimal volumes of the qRT-PCR reagents and to evaluate the validity and performance of four assays: Charité Berlin and European Virus Archive - GLOBAL (EVAg) primer-probe sets, and DAAN and Beijing Genomics Institute (BGI) premixed commercial kits. A multiplex and singleplex RT-PCR kit was used with the two primer-probe sets and the recommended assay volumes of the two premixed kits were altered. Results: In comparison to the multiplex RT-PCR kit, the singleplex RT-PCR kit combined with the primer-probe sets yielded consistent cycle threshold (Ct) values across the different titrations tested. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit showed incomparable Ct values and inconsistent results between batches using the manufacturer's recommended volumes. Conclusion: We achieved a 2.5-fold and 4-fold increase in the number of tests/kit for the premixed kits and the primer-probe sets, respectively. The primer-probe set assays were reliable and consistent, and we preferred a combination of an EVAg and a Berlin target. Any inconclusive result was repeated by different individuals following the same protocol. DAAN was a consistent and reliable assay even at lower concentrations from the stated recommendations. BGI in contrast, required dilution to improve its performance and was hence an assay that was used in combination with EVAg or Berlin targets.

Self-reported loss of smell without nasal obstruction to identify COVID-19. The multicenter Coranosmia cohort study

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Isolated loss of smell without nasal obstruction is an early red-flag of COVID-19.

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These patients should adopt all the preventive measures and a lockdown.

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Olfactory/gustative dysfunction had high predictive value to identify COVID-19.

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Olfactory/gustative dysfunction had high specificity to identify COVID-19.

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Self-reported loss of smell, among other symptoms, could help to screen COVID-19.

Objectives

To determine the frequency of SARS-CoV-2 positive samples in a subset of patients consulting for primarily isolated acute (<7 days) loss of smell and to assess the diagnostic accuracy of olfactory/gustatory dysfunction for COVID-19 diagnosis in the overall population tested for COVID-19 in the same period.

Methods

Prospective multicentric cohort study in four olfactory ENT units and a screening center for COVID-19.

Results

i) Among a subset of 55 patients consulting for primarily recent loss of smell, we found that 51 (92.7%) had a COVID-19 positive test (median viral load of 28.8 cycle threshold). Loss of smell was mostly total (anosmia), rarely associated with nasal obstruction but associated with a taste disorder in 80%. Olfactory dysfunction occurred suddenly, either as first complaint or preceded by mild symptoms occurring a median of 3 days. The majority of patients (72.9%) partially recovered the sense of smell within 15 days. ii) In a population of 1824 patients tested for COVID-19, the positive predictive value and the specificity of loss of smell and/or taste were 78.5% and 90.3% respectively (sensitivity (40.8%), negative predictive value (63.6%)).

Conclusions

Self-reported loss of smell had a high predictive positive value to identify COVID-19. Making this sign well known publicly could help to adopt isolation measures and inform potential contacts.

Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2

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BioFire Respiratory Panel 2.1 SARS-CoV-2 assay high sensitivity and specificity.

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Comparable performance to gold standard tests for low level viral RNA detection.

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Rapid, sample-to-answer, syndromic testing for respiratory pathogens with SARS-CoV-2.

We evaluated the performance of the BioFire® Respiratory Panel 2.1 (RP2.1) in the detection of SARS CoV-2 in comparison against three other SARS CoV-2 EUA assays. In these studies, the RP2.1 panel had 98 % positive percent agreement (48/49) and 100 % negative percent agreement (49/49). Since 30 % of nasopharyngeal swab specimens have a SARS CoV-2 Ct >30 and thus detection of virus in low titers is clinically relevant, a sample with a high titer was diluted and each 10 fold dilution was tested in triplicate and compared against 6 other EUA approved SARS CoV-2 assays. These data suggested that the BioFire® RP2.1 panel, along with four other SARS CoV-2 assays (Roche cobas, Cepheid Xpert Xpress, BioFire® Defense COVID19, and NECoV19), consistently detected viral RNA at the 10−7 dilution. Overall, these studies suggest that the BioFire® RP2.1 assay can be used to detect acute cases of SARS CoV2 in addition to patients with low viral titer later in disease presentation.

Serum IgM against SARS-CoV-2 correlates with in-hospital mortality in severe/critical patients with COVID-19 in Wuhan, China

Severe/critical patients with coronavirus disease 2019 (COVID-19) have become the central issue in the current global pandemic due to their high mortality rate. However, the relationship between antibody response and clinical outcomes has not been well described in this group. We conducted a single-center, retrospective, cohort study to investigate the relationship between serum immunoglobulin G (IgG) and IgM and clinical outcomes in severe/critical patients with COVID-19. Seventy-nine severe/critical patients with COVID-19 admitted in Wuhan Asia General Hospital in Wuhan, China during January 22, 2020 to March 6, 2020 were included. Serum antibodies were measured at day 25 (SD, 7) post illness onset. The median IgG titer was 113 (IQR 81-167) AU/ml, and IgM titer was 50 (IQR, 23-105) AU/ml. Patients whose IgM titer ≥ 50 AU/ml had higher in-hospital mortality (p=0.026). IgM titer ≥ 50 AU/ml was also correlated with higher incidences of Acute Respiratory Distress Syndrome (ARDS) and sepsis shock. Antibody remeasurements were performed in 42 patients, where IgM titer declined significantly in survivors (p=0.031). Serum IgM titer changes according to the COVID-19 progression. The severe/critical patients with COVID-19 have a higher risk of clinical adverse events when IgM titer ≥ 50 AU/ml. Further decreasing of IgM could imply a better outcome in severe/critical cases.

Evaluation of the Aptima™ transcription-mediated amplification assay (Hologic®) for detecting SARS-CoV-2 in clinical specimens

BACKGROUND

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which appeared in late 2019, has been limited by isolating infected individuals. However, identifying such individuals requires accurate diagnostic tools.

OBJECTIVE

This study evaluates the capacity of the Aptima™ Transcription-Mediated Amplification (TMA) assay (Hologic® Panther System) to detect the virus in clinical samples.

STUDY DESIGN

We compared the Aptima™ assay to two in-house real-time RT-PCR techniques, one running on the Panther Fusion™ module and the other on the MagNA Pure 96 and Light-Cycler 480 instruments. We included a total of 200 respiratory specimens: 100 tested prospectively and 100 retrospectively (25 -ve/75 +ve).

RESULTS

The final Cohen's kappa coefficients were: κ = 0.978 between the Aptima™ and Panther Fusion™ assays, κ = 0.945 between the Aptima™ and MagNA/LC480 assays and κ = 0.956 between the MagNA/LC480 and Panther Fusion™ assays.

CONCLUSION

These findings indicate that the Aptima™ SARS-CoV-2 TMA assay data agree well with those obtained with our routine methods and that this assay can be used to diagnose coronavirus disease 2019 (COVID-19).

A Challenging Colectomy for Acute Severe Ulcerative Colitis Complicated by COVID-19

We present the case of a patient with acute severe ulcerative colitis and concomitant COVID-19-related pneumonia who required a colectomy after a prolonged and complicated hospitalization during the initial stages of the SARS-CoV-2 pandemic, before the establishment of official procedures.

Utility of Available Methods for Diagnosing SARS-CoV-2 in Clinical Samples

: The laboratory diagnosis of SARS-CoV-2 should be done to confirm coronavirus disease 2019 (COVID-19) in suspected patients. Although several diagnostic methods have been developed in this regard, their accuracy for clinical application is not very clear yet. To compare the diagnostic value of laboratory tests for the detection of COVID-19 infection, this study provides an upcoming review of the newly developed detection methods. Sensitivity, specificity, detection limit, and turn-around-time of these methods are compared and challenges for their application in clinical settings are reviewed. PubMed and Google Scholar web sites were used for the systematic search until April 9, 2020 to identify the published studies based on the following keywords: “Detection”, “Coronavirus 2019”, “SARS-CoV-2”, and “Sensitivity”. Out of 526 results, a total of 54 articles, including 46 studies on detection methods, were considered eligible for the review. The results showed that most of the proposed tests focused on molecular methods, while immunological and point-of-care tests were investigated in 13 studies. There were also a few commercial automated methods for the qualitative detection of SARS-CoV-2 in clinical samples, most of which are not examined in the current review, as no data about their sensitivity and specificity were presented. Although the assessment of publication biases showed that 64% sensitivity and nearly 100% specificity for RT-PCR are close to reality, most of the related reports for serological methods are not valid and further studies are needed to confirm their utility in clinical settings. Moreover, the RT-PCR test alone cannot act as a gold standard because of bias in measurements. Therefore, antibody tests and other proposed methods could be used as supplementary diagnostic tests to improve RT-PCR accuracy. Although clinical findings are invaluable, in many cases, they can provide more valuable supportive data than serological tests.

Pitfalls in SARS-CoV-2 PCR diagnostics

To combat the COVID-19 pandemic, millions of PCR tests are performed worldwide. Any deviation of the diagnostic sensitivity and specificity will reduce the predictive values of the test. Here, we report the occurrence of contaminations of commercial primers/probe sets with the SARS-CoV-2 target sequence of the RT-qPCR as an example for pitfalls during PCR diagnostics affecting diagnostic specificity. In several purchased in-house primers/probe sets, quantification cycle values as low as 17 were measured for negative control samples. However, there were also primers/probe sets that displayed very low-level contaminations, which were detected only during thorough internal validation. Hence, it appears imperative to pre-test each batch of reagents extensively before use in routine diagnosis, to avoid false-positive results and low positive predictive value in low-prevalence situations. As such, contaminations may have happened more widely, and COVID-19 diagnostic results should be re-assessed retrospectively to validate the epidemiological basis for control measures.

The sensitivity of respiratory tract specimens for the detection of SARS-CoV-2: A protocol for a living systematic review and meta-analysis

Background

Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic. There is a clear need to establish a gold standard diagnostic for SARS-CoV-2 infection in humans using respiratory tract specimens.

Methods

Searches will be conducted in the bibliographic databases Medline, Embase, bioRxiv, medRxiv, F1000, ChemRxiv, PeerJ Preprints, Preprints.org, Beilstein Archive, and Research Square. Relevant government documents and grey literature will be sought on the FDA's Emergency Use Authorizations website, the ECDC's website, and the website of the Foundation for Innovative New Diagnostics. Finally, papers categorized as diagnosis papers by the EPPI Centre's COVID-19 living systematic map will be added to our screening process; those papers are tagged with the diagnosis topic based on human review, rather than database searches, and thus this set of papers might include ones that have not been captured by our search strategy.

COVID-19 in a patient with active tuberculosis: A rare case-report

Scarce data exist about the clinical features of COVID-19 in patients with concomitant active and/or latent tuberculosis (TB). This rare case-report outlines the diagnosis, management and outcome of a sixty year old hypertensive and diabetic patient with serious COVID-19 pneumonia and underlying active TB. The patient was treated successfully in a COVID-19 designated intensive care unit in Saudi Arabia.

Chest CT practice and protocols for COVID-19 from radiation dose management perspective

The global pandemic of coronavirus disease 2019 (COVID-19) has upended the world with over 6.6 million infections and over 391,000 deaths worldwide. Reverse-transcription polymerase chain reaction (RT-PCR) assay is the preferred method of diagnosis of COVID-19 infection. Yet, chest CT is often used in patients with known or suspected COVID-19 due to regional preferences, lack of availability of PCR assays, and false-negative PCR assays, as well as for monitoring of disease progression, complications, and treatment response. The International Atomic Energy Agency (IAEA) organized a webinar to discuss CT practice and protocol optimization from a radiation protection perspective on April 9, 2020, and surveyed participants from five continents. We review important aspects of CT in COVID-19 infection from the justification of its use to specific scan protocols for optimizing radiation dose and diagnostic information.

Key Points

• Chest CT provides useful information in patients with moderate to severe COVID-19 pneumonia.

• When indicated, chest CT in most patients with COVID-19 pneumonia must be performed with non-contrast, low-dose protocol.

• Although chest CT has high sensitivity for diagnosis of COVID-19 pneumonia, CT findings are non-specific and overlap with other viral infections including influenza and H1N1.

Considerations for the Surgical Management of Early Stage Lung Cancer During the COVID-19 Pandemic

The highly transmissible novel coronavirus (COVID-19) has infected over 8.8 million people globally and has upended the delivery of health care in the United States, creating unprecedented challenges to providing care to patients with early stage non–small cell lung cancer (NSCLC). The initial surge of patients with COVID-19 that have flooded hospitals has put a strain on physical space, workforce, and supplies. In addition, social distancing and the risk of COVID-19 transmission has created significant barriers for thoracic surgeons to diagnose and treat patients. Many hospitals across the country have temporarily suspended elective operations to preserve hospital beds, ventilators, and personal protective equipment. Currently, the pandemic has greatly disrupted the current standard of resection after adequate staging with imaging and/or surgical staging for early stage NSCLC well beyond the initial acute phase; therefore, a new paradigm for effective management will need to be devised until the COVID-19 pandemic is eradicated with systematic vaccination and herd immunity. Thoracic surgeons will need to recalibrate their approach to ensure that patients receive timely and effective treatment for early stage NSCLC. The management of early stage NSCLC during the COVID-19 pandemic should be balanced with available hospital resources, risk of progression of disease, risk of transmission of COVID-19 to patient and surgeon, and the availability of alternative therapies. This article will address the current challenges with treating early stage NSCLC during the COVID-19 pandemic and provide a clinical framework for providing effective surgical therapy while mitigating the risk of transmission of the SARS-CoV-2 virus to patients and surgeons.

A Perspective on Emerging Therapeutic Interventions for COVID-19

Coronaviruses are enveloped positive-sense RNA viruses with an unusual large RNA genome and a unique replication mechanism, which are characterized by club-like spikes that protrude from their surface. An outbreak of a novel coronavirus 2019 infection has posed significant threat to the health and economies in the whole world. This article reviewed the viral replication, pathogenicity, prevention and treatment strategies. With a lack of approved treatment options for this virus, alternative approaches to control the spread of disease is in urgent need. This article also covers some management strategies which may be applied to this virus outbreak. Ongoing clinical studies related to possible treatments for COVID-19, potential vaccines, and alternative medication such as natural compounds are also discussed.

SARS-CoV-2 productively infects human gut enterocytes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.

SARS-CoV-2 productively infects human gut enterocytes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.

Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco

Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19).

Here, we report a complete genome sequence obtained for a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from a nasopharyngeal swab specimen of a Moroccan patient with coronavirus disease 2019 (COVID-19).

Review of the SARS-CoV-2 in Wuhan and Analysis as Well as Prediction of Therapeutic Drugs

Due to the worldwide impact of SARS-CoV-2, people have carried out in-depth research on the virus to fight against this highly contagious disease. In this article, many articles published recently are summarized vertically, from the structure and sites of SARS-Cov-2, the mode of transmission, the mathematical model of transmission, the mechanism of the virus itself, the symptoms of patients after infection to medicine used in the early stage period and the prediction as well the analysis of probability in using new medicine.

Two Immunocompromised Patients With Diffuse Alveolar Hemorrhage as a Complication of Severe Coronavirus Disease 2019

Diffuse alveolar hemorrhage (DAH) is a severe and potentially life-threatening disease manifestation. In addition to autoimmune diseases such as antineutrophil cytoplasmic antibody-associated vasculitis and anti-glomerular basement membrane syndrome, pulmonary viral infections are known to be culprits of DAH. Health-care providers worldwide in the coronavirus disease 2019 pandemic have been confronted with an unprecedented number of viral lung infections, with great variance in symptoms and severity. Hemoptysis, the key symptom of DAH, is a rare complication. We present two cases of immunocompromised patients with rapidly developing hypoxemic respiratory failure and evidence of DAH in the context of severe acute respiratory syndrome coronavirus 2 infection.

COVID-19 Testing in Patients with Cancer: Does One Size Fit All?

The COVID-19 global pandemic has drastically impacted cancer care, posing challenges in treatment and diagnosis. There is increasing evidence that cancer patients, particularly those who have advanced age, significant comorbidities, metastatic disease, and/or are receiving active immunosuppressive therapy may be at higher risk of COVID-19 severe complications. Controlling viral spread from asymptomatic carriers in cancer centers is paramount, and appropriate screening methods need to be established. Universal testing of asymptomatic cancer patients may be key to ensure safe continuation of treatment and appropriate hospitalized patients cohorting during the pandemic. Here we perform a comprehensive review of the available evidence regarding SARS-CoV-2 testing in asymptomatic cancer patients, and describe the approach adopted at Princess Margaret Cancer Centre (Toronto, Canada) as a core component of COVID-19 control.

Influence of Storage Conditions on SARS-CoV-2 Nucleic Acid Detection in Throat Swabs

The detection of SARS-CoV-2 infection is the premise of quarantine. In many countries or areas, samples need to be shipped or inactivated before SARS-CoV-2 testing. In this study, we checked the influence of sample storage conditions on SARS-CoV-2 nucleic acid testing results, including sample inactivation time, storage temperature, and storage time. All of these conditions caused an increase in the cycle threshold values of the nucleic acid tests and led to the misclassification of at least 10.2% of positive cases as negative or suspected. The results highlight the importance of immediate testing of samples for SARS-CoV-2 nucleic acid detection.

Prevalence of SARS-CoV-2 specific neutralising antibodies in blood donors from the Lodi Red Zone in Lombardy, Italy, as at 06 April 2020

We evaluated SARS-CoV-2 RNA and neutralising antibodies in blood donors (BD) residing in the Lodi Red Zone, Italy. Of 390 BDs recruited after 20 February 2020 − when the first COVID-19 case in Lombardy was identified, 91 (23%) aged 19–70 years were antibody positive. Viral RNA was detected in an additional 17 (4.3%) BDs, yielding ca 28% (108/390) with evidence of virus exposure. Five stored samples collected as early as 12 February were seropositive.

Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: A Feasibility Study

The COVID-19 pandemia due to the SARS-CoV-2 coronavirus, in its first 4 months since its outbreak, has to date reached more than 200 countries worldwide with more than 2 million confirmed cases (probably a much higher number of infected), and almost 200,000 deaths. Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Thus there is a need for alternative, faster, less expensive and more accessible tests. We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. Of these patients, 177 resulted positive, whereas 102 received a negative response. We have developed two machine learning models, to discriminate between patients who are either positive or negative to the SARS-CoV-2: their accuracy ranges between 82% and 86%, and sensitivity between 92% e 95%, so comparably well with respect to the gold standard. We also developed an interpretable Decision Tree model as a simple decision aid for clinician interpreting blood tests (even off-line) for COVID-19 suspect cases. This study demonstrated the feasibility and clinical soundness of using blood tests analysis and machine learning as an alternative to rRT-PCR for identifying COVID-19 positive patients. This is especially useful in those countries, like developing ones, suffering from shortages of rRT-PCR reagents and specialized laboratories. We made available a Web-based tool for clinical reference and evaluation (This tool is available at https://covid19-blood-ml.herokuapp.com/ ).

A single centre study of viral community-acquired pneumonia in children: No evidence of SARS-CoV-2 from October 2019 to March 2020

Pneumonia is an important cause of morbidity and mortality in children. We described viral aetiologies, with particular interest in detecting SARS-CoV-2, in hospitalized pneumonia children. Human rhinovirus was the most frequently detected agent. No children tested positive for SARS-CoV-2. Our findings suggest that SARS-CoV-2 infection is rare in children and it was not circulating in Rome before COVID-19 outbreak.

How to Determine When SARS-CoV-2 Antibody Testing Is or Is Not Useful for Population Screening: A Tutorial

Extensive testing lies at the heart of any strategy to effectively combat the SARS-COV-2 pandemic. In recent months, the use of enzyme-linked immunosorbent assay-based antibody tests has gained a lot of attention. These tests can potentially be used to assess SARS-COV-2 immunity status in individuals (e.g., essential health care personnel). They can also be used as a screening tool to identify people that had COVID-19 asymptomatically, thus getting a better estimate of the true spread of the disease, gain important insights on disease severity, and to better evaluate the effectiveness of policy measures implemented to combat the pandemic. But the usefulness of these tests depends not only on the quality of the test but also, critically, on how far disease has already spread in the population. For example, when only very few people in a population are infected, a positive test result has a high chance of being a false positive. As a consequence, the spread of the disease in a population as well as individuals' immunity status may be systematically misinterpreted. SARS-COV-2 infection rates vary greatly across both time and space. In many places, the infection rates are very low but can quickly skyrocket when the virus spreads unchecked. Here, we present two tools, natural frequency trees and positive and negative predictive value graphs, that allow one to assess the usefulness of antibody testing for a specific context at a glance. These tools should be used to support individual doctor-patient consultation for assessing individual immunity status as well as to inform policy discussions on testing initiatives.

Un cas de COVID-19 compliqué d´embolie avec deux tests PCR initialement négatifs malgré des signes scanographiques

La maladie à coronavirus 2019 (COVID-19) déclarée en Chine en fin 2019 s´est rapidement généralisée aux autres continents. Son diagnostic se fait par test PCR (Polymerase Chain Reaction) sur des prélèvements naso-pharyngés. Ce test bien que spécifique est d´une sensibilité moindre comparé à la TDM thoracique. Nous rapportons le cas d´un patient testé négatif à deux reprises et chez qui la TDM retrouvait des signes typiques de COVID-19 et une embolie pulmonaire. Et ce n´est qu´après un troisième test PCR qu´il a été positif. Ce qui montre l´intérêt de répéter plusieurs fois les tests PCR mais également de considérer les signes scanographiques comme argument diagnostic devant induire une prise en charge adéquate.

The relationship between diagnostic value of chest computed tomography imaging and symptom duration in COVID infection

OBJECTIVES

Severe acute respiratory syndrome-coronovirus-2 is a global public health problem, in which early diagnosis is required to prevent the spread of infection. In this study, we aimed to reveal the diagnostic value of chest computed tomography (CT) imaging with respect to symptom duration.

METHODS

This retrospective study involved patients from five centers, who were admitted with typical COVID-19 symptoms and found to be positive for COVID-19 real-time reverse transcription-polymerase chain reaction (rtRT-PCR) test.

RESULTS

One hundred and five patients with positive COVID-19 rtRT-PCR test were involved in the study. Sixty percent of these patients had chest CT imaging findings consistent with COVID-19 pneumonia. The most common chest CT finding was bilateral and subpleural ground-glass opacity in middle-lower lobes of the lungs. Chest CT findings were detected in 85.1% of the patients with a symptom duration of more than 2 days. In receiver operating characteristic analysis of this parameter, area under the curve (AUC) was 0.869, while sensitivity and specificity were 90.5% and 76.2%, respectively. It was notable that chest CT findings were 7.17 times more common among the patients aged 60 years and older, with AUC, specificity, and positive predictive value of 0.768, 88.1%, and 84.8%, respectively.

CONCLUSION

Chest CT imaging is a quite valuable tool in patients with longer than 2 days' duration of symptoms, in whom clinical and epidemiological data support the diagnosis of COVID-19 infection. We suggest that the diagnosis of COVID-19 pneumonia should be made with chest CT imaging when rtRT-PCR test cannot be performed or gives a negative result, which is important for public health and to prevent the spread of infection.

Risk Assessment and Prevention of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission for Hospitalized Urological Patients After the COVID-19 Pandemic in Wuhan, China

BACKGROUND

Emerging asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were detected and multiple cases were found to be SARS-CoV-2 positive again, which raised an alarm for the patients hospitalized after the coronavirus disease 2019 (COVID-19) pandemic.

OBJECTIVE

We investigated the risk and prevention of hospital transmission of SARS-CoV-2 to hospitalized urological patients.

DESIGN SETTING AND PARTICIPANTS

This is a retrospective study of 319 hospitalized urological patients enrolled between April 20, 2020 and May 11, 2020 from two tertiary hospitals in Wuhan, China.

INTERVENTION

Chest computed tomography (CT) images, nucleic acid tests (NATs), and serum antibody were examined at the outpatient department and 1 wk after admission for all patients.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The chest CT images, NATs, serum antibody results, and clinical data were collected and analyzed.

RESULTS AND LIMITATIONS

None of the 319 patients was found to be SARS-CoV-2 NAT positive. Ten and four patients were detected to be immunoglobulin (Ig)G and IgM positive, respectively. The chest CT features of 116 patients showed abnormal lung findings. During the 1-wk isolation, one patient initially being IgG positive only was found to be IgM positive, and another initially IgM-positive patient had a rising IgG level. Through risk assessment, we identified seven patients with very high and high risk for hospital transmission, and delayed the surgery while maintaining close follow-up. Five intermediate-risk patients were operated on successfully under paravertebral block or epidural anesthesia to avoid opening the airway with endotracheal intubation. The remaining 104 low-risk and 203 normal patients underwent normal surgery.

CONCLUSIONS

Of the 319 patients, seven were identified as very high and high risk, which reinforced the importance of epidemic surveillance of discharged COVID-19 patients and asymptomatic infections. Five intermediate-risk patients were operated on successfully under regional anesthesia.

PATIENT SUMMARY

Our experience of risk assessment and management practice may provide a strategy to prevent severe acute respiratory syndrome coronavirus 2 transmission to hospitalized urological patients after the coronavirus disease 2019 (COVID-19) pandemic.

Laboratory diagnosis of SARS-CoV-2: available approaches and limitations

The ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the most devastating outbreaks witnessed in the last 100 years. The outbreak started in China and spread rapidly to almost every country, culminating in woefully overwhelmed health-care systems in most countries. The only approved diagnostic test to accompany radiographic evaluation is reverse transcription PCR. However, the applicability of this test in diagnosis and surveillance is challenged by a global shortage of reagents and the lack of well-equipped laboratories with specialized staff in several low- and middle-income countries. Loop-mediated isothermal amplification and CRISPR-based diagnostic assays have developed and expected to play a role however, their accuracy is still inferior to the recommended PCR approach. The need for the development of accurate and rapid diagnostic assays became apparent. Immunodiagnostic tests and other molecular approaches were developed and tested. Other recently developed point-of-care molecular tests are expected to be helpful in pandemic management as no particular skills are required from the operator. Fortunately, a number of serological tests have been granted authorization for use under the emergency situation by the US FDA for the diagnosis of SARS-CoV-2. The majority of recently authorized serological tests detect IgG and IgM in blood of infected individuals by on ELISA, chemiluminescence platforms or lateral flow cassettes.

A deep dive into testing and management of COVID-19 for Australian high performance and professional sport

The purpose of testing for any communicable disease is to support clinicians in the diagnosis and management of individual patients and to describe transmission dynamics. The novel coronavirus is formally named SARS-CoV-2 and the clinical disease state resulting from an infection is known as COVID-19. Control of the COVID-19 pandemic requires clinicians, epidemiologists, and public health officials to utilise the most comprehensive, accurate and timely information available to manage the rapidly evolving COVID-19 environment. High performance sport is a unique context that may look towards comprehensive testing as a means of risk mitigation. Characteristics of the common testing options are discussed including the circumstances where additional testing may be of benefit and considerations for the associated risks. Finally, a review of the available technology that could be considered for use by medical staff at the point of care (PoC) in a high-performance sporting context is included.

Rapid implementation and validation of a cold-chain free SARS-CoV-2 diagnostic testing workflow to support surge capacity

BACKGROUND

In January 2020 reports of unidentified severe respiratory illness were described in Wuhan, China. A rapid expansion in cases affecting most countries around the globe led to major changes in the way people live their daily lives. In the United Kingdom, the Department of Health and Social Care directed healthcare providers to establish additional resources to manage the anticipated surge in cases that could overwhelm the health services. A priority area was testing for SARS-CoV-2 RNA and its detection by qualitative RT-PCR.

DESIGN

A laboratory workflow twinning research environment with clinical laboratory capabilities was implemented and validated in the University of Birmingham within 4 days of the project initiation. The diagnostic capability was centred on an IVD CE-marked RT-PCR kit and designed to provide surge capacity to the nearby Queen Elizabeth Hospital. The service was initially tasked with testing healthcare workers (HCW) using throat swabs, and subsequently the process investigated the utility of using saliva as an alternative sample type.

RESULTS

Between the 8th April 2020 and the 30th April 2020, the laboratory tested a total of 1282 HCW for SARS-CoV-2 RNA in throat swabs. RNA was detected in 54 % of those who reported symptoms compatible with COVID-19, but in only 4% who were asymptomatic.

CONCLUSION

This capability was established rapidly and utilised a cold-chain free methodology, applicable to a wide range of settings, and which can provide surge capacity and support to clinical laboratories facing increasing pressure during periods of national crisis.

Steps, implementation and importance of quality management in diagnostic laboratories with special emphasis on coronavirus disease-2019

A well-established and functional quality management system is an integral part of any diagnostic laboratory. It assures the reliability and standards of the laboratory function. A pandemic situation such as that caused by the influenza H1N1 2009 virus or the recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) increases the demands on the public health system, and the need to build, upgrade and expand the number of diagnostic laboratories. The Coronavirus disease-19 (COVID-19) pandemic caused by the SARS-CoV-2 unleashed a public health emergency of an unprecedented scale. The need has been highlighted for the accreditation of tests relating to COVID-19 by the National Accreditation Board for Testing and Calibration Laboratories (NABL) or any agencies approved by the World Health Organization (WHO) or Indian Council of Medical Research. The implementation of quality system in diagnostic laboratories would ensure accurate, reliable and efficient test results at par with the international standards. The functional aspects of a laboratory such as a well-defined organogram, standard operating procedures, good laboratory practices, quality controls, human resources, equipment management, reagents, inventory of records, proper communication need to be addressed to assure quality. Biosafety considerations should include the guidelines laid out by the WHO, the Institutional Biosafety Committee and the Department of Biotechnology, Government of India for carrying out diagnostic work in the laboratory. Currently, there are 1922 laboratories, operational for COVID-19 diagnosis in India. Considering the urgency of testing, the NABL has expedited the process of accreditation and issued accreditation to 818 laboratories. The adherence to the practicable aspects of quality described in this article would help in establishing quality in COVID-19 testing laboratories.

Rapid Development and Validation of a Novel Laboratory-Derived Test for the Detection of SARS-CoV-2

Objectives

To increase testing capability for SARS-CoV-2 during a rapidly evolving public health emergency, we aimed to deploy a validated laboratory-developed real-time reverse transcription polymerase chain reaction (RT-PCR) diagnostic test for SARS-CoV-2 on an accelerated timeline and using reagent supply chains that were not constrained.

Methods

A real-time RT-PCR assay that detects the structural envelope (E) gene of SARS-CoV-2 was developed and validated on the Roche cobas 6800 instrument platform with the omni Utility channel reagents, which performs automated nucleic acid extraction and purification, PCR amplification, and detection. In silico analysis was performed for both inclusivity of all SARS-CoV-2 variants and cross reactivity with other pathogenic organisms. Positive control material was used to determine the Limit of Detection (LOD) and patient samples (positive and negative) confirmed by another authorized assay were used for clinical validation. Experiments were carried out at the Christiana Care Health System’s Molecular Diagnostics Laboratory (Newark, DE) between April 1 and April 4, 2020.

Results

A real-time RT-PCR assay for SARS-Cov-2 was developed and validated in just two weeks. For all oligonucleotides, 100% homology to the available SARS-CoV-2 sequences was observed. Greater than 80% homology between one or more oligonucleotides was observed for SARS-Cov (Urbani strain) and Influenza A, however risk of cross reactivity was deemed to be low. The limit of detection (LOD) of the assay was 250 copies/mL. The assay identified 100% of positive patient samples (30/30) and 100% of negative patient samples (29/29 patient negatives and 1/1 saline). Up to 92 samples can be run on a single plate and analysis takes approximately 3.5 hours.

Conclusions

In this work, we demonstrate the development and validation of a single target laboratory-developed test for SARS-CoV-2 in two weeks. Key considerations for complementary supply chains enabled development on an accelerated timeline and an increase in testing capability.

CT imaging features of 4121 patients with COVID-19: A meta-analysis

OBJECTIVE

We systematically reviewed the computed tomography (CT) imaging features of coronavirus disease 2019 (COVID-19) to provide reference for clinical practice.

METHODS

Our article comprehensively searched PubMed, FMRS, EMbase, CNKI, WanFang databases, and VIP databases to collect literatures about the CT imaging features of COVID-19 from 1 January to 16 March 2020. Three reviewers independently screened literature, extracted data, and assessed the risk of bias of included studies, and then, this meta-analysis was performed by using Stata12.0 software.

RESULTS

A total of 34 retrospective studies involving a total of 4121 patients with COVID-19 were included. The results of the meta-analysis showed that most patients presented bilateral lung involvement (73.8%, 95% confidence interval [CI]: 65.9%-81.1%) or multilobar involvement (67.3%, 95% CI: 54.8%-78.7%) and just little patients showed normal CT findings (8.4%). We found that the most common changes in lesion density were ground-glass opacities (68.1%, 95% CI: 56.9%-78.2%). Other changes in density included air bronchogram sign (44.7%), crazy-paving pattern (35.6%), and consolidation (32.0%). Patchy (40.3%), spider web sign (39.5%), cord-like (36.8%), and nodular (20.5%) were common lesion shapes in patients with COVID-19. Pleural thickening (27.1%) was found in some patients. Lymphadenopathy (5.4%) and pleural effusion (5.3%) were rare.

CONCLUSION

The lung lesions of patients with COVID-19 were mostly bilateral lungs or multilobar involved. The most common chest CT findings were patchy and ground-glass opacities. Some patients had air bronchogram, spider web sign, and cord-like. Lymphadenopathy and pleural effusion were rare.

Community-acquired viral respiratory infections amongst hospitalized inpatients during a COVID-19 outbreak in Singapore: co-infection and clinical outcomes

AIMS

During the ongoing COVID-19 outbreak, co-circulation of other common respiratory viruses can potentially result in co-infections; however, reported rates of co-infections for SARS-CoV-2 vary. We sought to evaluate the prevalence and etiology of all community acquired viral respiratory infections requiring hospitalization during an ongoing COVID-19 outbreak, with a focus on co-infection rates and clinical outcomes.

METHODS

Over a 10-week period, all admissions to our institution, the largest tertiary hospital in Singapore, were screened for respiratory symptoms, and COVID-19 as well as a panel of common respiratory viral pathogens were systematically tested for. Information was collated on clinical outcomes, including requirement for mechanical ventilation and in hospital mortality.

RESULTS

One-fifth (19.3%, 736/3807) of hospitalized inpatients with respiratory symptoms had a PCR-proven viral respiratory infection; of which 58.5% (431/736) tested positive for SARS-CoV-2 and 42.2% (311/736) tested positive for other common respiratory viruses. The rate of co-infection with SARS-CoV-2 was 1.4% (6/431); all patients with co-infection had mild disease and stayed in communal settings. The in-hospital mortality rate and proportion of COVID-19 patients requiring invasive ventilation was low, at around 1% of patients; these rates were lower than patients with other community-acquired respiratory viruses admitted over the same period (p < 0.01).

CONCLUSION

Even amidst an ongoing COVID-19 outbreak, common respiratory viruses still accounted for a substantial proportion of hospitalizations. Coinfections with SARS-CoV-2 were rare, with no observed increase in morbidity or mortality.

[Seroprevalence and SARS-CoV-2 testing in healthcare occupations]

The SARS-CoV‑2 causes a disease spectrum that includes asymptomatic and mildly symptomatic infections with subclinical manifestations but which can nevertheless still be potentially contagious. Evidence from SARS-CoV‑2 infected macaque monkeys and from studies with seasonal coronaviruses suggests that the infection is likely to produce an immunity that is protective for a certain period of time. Available test methods enable a high degree of reliability, e.g. if high-quality serological methods are combined. Although individual test results have to be interpreted with caution, serosurveillance in a tertiary eye care center and large eye research institute can reduce anxiety and provide clarity regarding the actual number of (unreported) SARS-CoV‑2 infections.

Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: A Feasibility Study

The COVID-19 pandemia due to the SARS-CoV-2 coronavirus, in its first 4 months since its outbreak, has to date reached more than 200 countries worldwide with more than 2 million confirmed cases (probably a much higher number of infected), and almost 200,000 deaths. Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Thus there is a need for alternative, faster, less expensive and more accessible tests. We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. Of these patients, 177 resulted positive, whereas 102 received a negative response. We have developed two machine learning models, to discriminate between patients who are either positive or negative to the SARS-CoV-2: their accuracy ranges between 82% and 86%, and sensitivity between 92% e 95%, so comparably well with respect to the gold standard. We also developed an interpretable Decision Tree model as a simple decision aid for clinician interpreting blood tests (even off-line) for COVID-19 suspect cases. This study demonstrated the feasibility and clinical soundness of using blood tests analysis and machine learning as an alternative to rRT-PCR for identifying COVID-19 positive patients. This is especially useful in those countries, like developing ones, suffering from shortages of rRT-PCR reagents and specialized laboratories. We made available a Web-based tool for clinical reference and evaluation (This tool is available at https://covid19-blood-ml.herokuapp.com/ ).