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1.
JCI Insight ; 5(10)2020 05 21.
Article in English | MEDLINE | ID: covidwho-687860

ABSTRACT

BACKGROUNDThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a novel viral pneumonia (COVID-19), which is rapidly spreading throughout the world. The positive result of nucleic acid test is a golden criterion to confirm SARS-CoV-2 infection, but the detection features remain unclear.METHODSWe performed a retrospective analysis in 5630 high-risk individuals receiving SARS-CoV-2 nucleic acid tests in Wuhan, China, and investigated their characteristics and diagnosis rates.RESULTSThe overall diagnosis rate was 34.7% (1952/5630). Male (P = 0.025) and older populations (P = 2.525 × 10-39) were at significantly higher risk of SARS-CoV-2 infection. People were generally susceptible, and most cases concentrated in people of 30-79 years. Furthermore, we investigated the association between diagnosis rate and the amount of testing in 501 subjects. Results revealed a 1.27-fold improvement (from 27.9% to 35.5%) of diagnosis rate from testing once to twice (P = 5.847 × 10-9) and a 1.43-fold improvement (from 27.9% to 39.9%) from testing once to 3 times (P = 7.797 × 10-14). More than 3 testing administrations was not helpful for further improvement. However, this improvement was not observed in subjects with pneumonia (P = 0.097).CONCLUSIONAll populations are susceptible to SARS-CoV-2 infection, and male and older-aged populations are at significantly higher risk. Increasing the amount of testing could significantly improve diagnosis rates, except for subjects with pneumonia. It is recommended to test twice in those high-risk individuals whose results are negative the first time, and performing 3 tests is better, if possible.FUNDINGThis work was supported by National Mega Project on Major Infectious Disease Prevention (no. 2017ZX10103005-007) and National Key Research and Development Program of China (no. 2018YFE0204500).


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Child , Child, Preschool , China/epidemiology , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Female , Humans , Incidence , Infant , Infant, Newborn , Male , Middle Aged , Molecular Diagnostic Techniques , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Retrospective Studies , Sex Factors , Young Adult
2.
PLoS One ; 15(7): e0236564, 2020.
Article in English | MEDLINE | ID: covidwho-676213

ABSTRACT

To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR to detect SARS-CoV-2 in nasopharyngeal swabs without RNA extraction. Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. The results were compared to that of standard approach that involves RNA extraction. Incubation of specimens at 65°C for 10 minutes along with the use of TaqPath™ 1-Step RT-qPCR Master Mix provides higher analytical sensitivity for detection of SARS-CoV-2 RNA than many other conditions tested. The optimized direct RT-qPCR approach demonstrated a limit of detection of 6.6x103 copy/ml and high reproducibility (co-efficient of variation = 1.2%). In 132 nasopharyngeal specimens submitted for SARS-CoV-2 testing, the sensitivity, specificity and accuracy of our optimized approach were 95%, 99% and 98.5%, respectively, with reference to the standard approach. Also, the RT-qPCR CT values obtained by the two methods were positively correlated (Pearson correlation coefficient r = 0.6971, p = 0.0013). The rate of PCR inhibition by the direct approach was 8% compared to 9% by the standard approach. Our simple approach to detect SARS-CoV-2 RNA by direct RT-qPCR may help laboratories continue testing for the virus despite reagent shortages or expand their testing capacity in resource limited settings.


Subject(s)
Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Specimen Handling/methods , Betacoronavirus , Humans , Nasopharynx/virology , Pandemics , Reproducibility of Results , Sensitivity and Specificity
3.
Int J Mol Med ; 46(3): 957-964, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-676117

ABSTRACT

Reverse transcription­quantitative polymerase chain reaction (RT­qPCR) is the gold standard method for the diagnosis of COVID­19 infection. Due to pre­analytical and technical limitations, samples with low viral load are often misdiagnosed as false­negative samples. Therefore, it is important to evaluate other strategies able to overcome the limits of RT­qPCR. Blinded swab samples from two individuals diagnosed positive and negative for COVID­19 were analyzed by droplet digital PCR (ddPCR) and RT­qPCR in order to assess the sensitivity of both methods. Intercalation chemistries and a World Health Organization (WHO)/Center for Disease Control and Prevention (CDC)­approved probe for the SARS­CoV­2 N gene were used. SYBR­Green RT­qPCR is not able to diagnose as positive samples with low viral load, while, TaqMan Probe RT­qPCR gave positive signals at very late Ct values. On the contrary, ddPCR showed higher sensitivity rate compared to RT­qPCR and both EvaGreen and probe ddPCR were able to recognize the sample with low viral load as positive even at 10­fold diluted concentration. In conclusion, ddPCR shows higher sensitivity and specificity compared to RT­qPCR for the diagnosis of COVID­19 infection in false­negative samples with low viral load. Therefore, ddPCR is strongly recommended in clinical practice for the diagnosis of COVID­19 and the follow­up of positive patients until complete remission.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Humans , Nucleocapsid Proteins/genetics , Pandemics , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
4.
AIDS Res Ther ; 17(1): 46, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-671088

ABSTRACT

BACKGROUND: The COVID-19 has been a severe pandemic all around the world. Nowadays the patient with co-infection of HIV and SARS-CoV-2 was rarely reported. Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. CASE PRESENTATION: The patient was infected with HIV 8 years ago through sexual transmission and had the normal CD4+T cell count. She was found SARS-CoV-2 positive using real-time Polymerase Chain Reaction (RT-PCR) during the epidemic. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. CONCLUSION: The viral shedding duration may be prolonged in people living with HIV. The 14 days isolation strategy might not be long enough for them. The isolation or discharge of these patients needs further confirmation for preventing epidemics.


Subject(s)
Anti-Retroviral Agents/therapeutic use , Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , HIV Infections/complications , Pneumonia, Viral/diagnosis , Virus Shedding , Benzoxazines/administration & dosage , Betacoronavirus/genetics , Betacoronavirus/immunology , C-Reactive Protein/analysis , CD4 Lymphocyte Count , Chills , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/drug therapy , Fatigue , Female , Fever , HIV/growth & development , HIV Infections/drug therapy , HIV Infections/immunology , Humans , Immunocompromised Host , Immunoglobulin M/blood , Lamivudine/administration & dosage , Middle Aged , Pandemics , Pharyngitis , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/drug therapy , Real-Time Polymerase Chain Reaction , Sputum/virology , Time Factors , Tomography, X-Ray Computed , Virus Shedding/immunology , Zidovudine/administration & dosage
5.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-670471

ABSTRACT

In early March 2020, the University of Washington Medical Center clinical virology laboratory became one of the first clinical laboratories to offer testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). When we first began test development in mid-January, neither of us believed there would be more than 2 million confirmed SARS-CoV-2 infections nationwide or that we would have performed more than 150,000 real-time PCR (RT-PCR) tests, with many more to come. This article will be a chronological summary of how we rapidly validated tests for SARS-CoV-2, increased our testing capacity, and addressed the many problems that came up along the way.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Academic Medical Centers , Capacity Building , Diagnostic Services/organization & administration , Humans , Pandemics , Universities , Washington
7.
Euro Surveill ; 25(27)2020 07.
Article in English | MEDLINE | ID: covidwho-652787

ABSTRACT

Laboratory preparedness with quality-assured diagnostic assays is essential for controlling the current coronavirus disease (COVID-19) outbreak. We conducted an external quality assessment study with inactivated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to support clinical laboratories with a proficiency testing option for molecular assays. To analyse SARS-CoV-2 testing performance, we used an online questionnaire developed for the European Union project RECOVER to assess molecular testing capacities in clinical diagnostic laboratories.


Subject(s)
Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Coronavirus/isolation & purification , Molecular Diagnostic Techniques/methods , Pandemics , Pneumonia, Viral/diagnosis , Betacoronavirus , Clinical Laboratory Services , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Disease Outbreaks , Europe , Humans , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Real-Time Polymerase Chain Reaction/standards , Reverse Transcriptase Polymerase Chain Reaction/standards , Sensitivity and Specificity , Surveys and Questionnaires
8.
BMC Infect Dis ; 20(1): 517, 2020 Jul 16.
Article in English | MEDLINE | ID: covidwho-651422

ABSTRACT

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a public health emergency of major international concern. Real-time RT-PCR assays are recommended for diagnosis of COVID-19. Here we report a rare case of COVID-19 with multiple negative results for PCR assays outside Wuhan, China. CASE PRESENTATION: A 32-year old male was admitted to our hospital because of 6 days of unexplained fever on January 29, 2020. He had come from Wuhan city 10 days before admission. Five days before admission, no abnormality was noted in laboratory test, chest radiography, and nasopharyngeal swab test for the SARS-CoV-2 nucleic acid. The patient was treated with ibuprofen for alleviating fever. On admission, chest computed tomography showed multiple ground-glass opacities in right lower lung field. COVID-19 was suspected. Three times of nasopharyngeal swab specimens were collected after admission. However, none of the specimens were positive. The patient was confirmed with COVID-19 after fifth SARS-CoV-2 nucleic acid test. He was treated with lopinavir/ritonavir, recombinant human interferon alfa-2b inhalation, methylprednisolone. After 18 days of treatment, he was discharged with improved symptoms, lung lesions and negative results of nasopharyngeal swab. CONCLUSION: This case reminds clinician that a patient with high clinical suspicion of COVID-19 but multiple negative RT-PCR result should not be taken out of isolation. A combination of patient's exposure history, clinical manifestations, laboratory tests, and typical imaging findings plays a vital role in making preliminary diagnosis and guide early isolation and treatment. Repeat swab tests are helpful in diagnosis for this kind of patients.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Negative Results , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Adult , Betacoronavirus/genetics , China/epidemiology , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/physiopathology , Fever/etiology , Fever/virology , Hospitalization , Humans , Male , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/physiopathology , Quarantine , Radiography , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Tomography, X-Ray Computed , Uncertainty
9.
J Infect Dis ; 222(2): 189-193, 2020 06 29.
Article in English | MEDLINE | ID: covidwho-643587

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel ß-coronavirus, causes severe pneumonia and has spread throughout the globe rapidly. The disease associated with SARS-CoV-2 infection is named coronavirus disease 2019 (COVID-19). To date, real-time reverse-transcription polymerase chain reaction (RT-PCR) is the only test able to confirm this infection. However, the accuracy of RT-PCR depends on several factors; variations in these factors might significantly lower the sensitivity of detection. METHODS: In this study, we developed a peptide-based luminescent immunoassay that detected immunoglobulin (Ig)G and IgM. The assay cutoff value was determined by evaluating the sera from healthy and infected patients for pathogens other than SARS-CoV-2. RESULTS: To evaluate assay performance, we detected IgG and IgM in the sera from confirmed patients. The positive rate of IgG and IgM was 71.4% and 57.2%, respectively. CONCLUSIONS: Therefore, combining our immunoassay with real-time RT-PCR might enhance the diagnostic accuracy of COVID-19.


Subject(s)
Antibodies, Viral/blood , Betacoronavirus/immunology , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Immunoenzyme Techniques/methods , Pneumonia, Viral/diagnosis , Serologic Tests/methods , Adult , Coronavirus Infections/immunology , Female , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Luminescent Measurements , Male , Middle Aged , Pandemics , Peptides/immunology , Pneumonia, Viral/immunology , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Viral Proteins/immunology
10.
Front Cell Infect Microbiol ; 10: 356, 2020.
Article in English | MEDLINE | ID: covidwho-642075

ABSTRACT

CDC and WHO guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis only recommend synthetic fiber swabs for nasopharyngeal (NP) sampling. We show that cotton-tipped plastic swabs do not inhibit PCR and have equivalent performance to rayon swabs. Cotton-tipped plastic swabs are massively produced worldwide and would prevent swab supply shortages under the current high SARS-CoV-2 testing demands, particularly in developing countries.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/instrumentation , Coronavirus Infections/diagnosis , Diagnostic Equipment/supply & distribution , Disposable Equipment/supply & distribution , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/instrumentation , Betacoronavirus/genetics , Cellulose/supply & distribution , Clinical Laboratory Techniques/methods , Coronavirus Infections/virology , Cotton Fiber/supply & distribution , Humans , Nasopharynx , Pandemics , Plastics/supply & distribution , Pneumonia, Viral/virology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction/methods , Specimen Handling/instrumentation , Specimen Handling/methods
11.
Theranostics ; 10(16): 7150-7162, 2020.
Article in English | MEDLINE | ID: covidwho-639991

ABSTRACT

In December 2019, a new coronavirus disease (COVID-19) outbreak occurred in Wuhan, China. Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which is the seventh coronavirus known to infect humans, is highly contagious and has rapidly expanded worldwide since its discovery. Quantitative nucleic acid testing has become the gold standard for diagnosis and guiding clinical decisions regarding the use of antiviral therapy. However, the RT-qPCR assays targeting SARS-CoV-2 have a number of challenges, especially in terms of primer design. Primers are the pivotal components of a RT-qPCR assay. Once virus mutation and recombination occur, it is difficult to effectively diagnose viral infection by existing RT-qPCR primers. Some primers and probes have also been made available on the WHO website for reference. However, no previous review has systematically compared the previously reported primers and probes and described how to design new primers in the event of a new coronavirus infection. This review focuses on how primers and probes can be designed methodically and rationally, and how the sensitivity and specificity of the detection process can be improved. This brief review will be useful for the accurate diagnosis and timely treatment of the new coronavirus pneumonia.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , RNA/genetics , Real-Time Polymerase Chain Reaction/methods , Base Sequence , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Drug Design , Genes, Viral , Humans , Nucleic Acid Conformation , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , RNA/chemistry , RNA Probes/genetics , RNA, Viral/chemistry , Real-Time Polymerase Chain Reaction/statistics & numerical data , Sensitivity and Specificity , Theranostic Nanomedicine
12.
J Korean Med Sci ; 35(26): e246, 2020 Jul 06.
Article in English | MEDLINE | ID: covidwho-634802

ABSTRACT

There is still a paucity of studies on real-world outcome of screening clinic for hospital protection from coronavirus disease 2019 (COVID-19). As the number of COVID-19 cases was growing rapidly in Daegu, Korea, we started operating an active screening clinic outside the hospital premises. Over two weeks, 2,087 patients were screened using real-time reverse transcriptase polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2, with 42 confirmed cases. Before the screening clinic period, an average of 36 beds (maximum 67 beds) per day were closed due to unrecognized COVID-19 patients entering the hospital. In contrast, after the screening clinic operated well, only one event of closing emergency room (25 beds) occurred due to a confirmed COVID-19 case of asymptomatic patient. We report the operational process of screening clinic for COVID-19 and its effectiveness in maintaining the function of tertiary hospitals.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Cross Infection/prevention & control , Mass Screening/methods , Pandemics/prevention & control , Pneumonia, Viral/diagnosis , Pneumonia, Viral/prevention & control , Ambulatory Care Facilities , Betacoronavirus/genetics , Emergency Service, Hospital , Humans , Real-Time Polymerase Chain Reaction , Republic of Korea , Reverse Transcriptase Polymerase Chain Reaction , Tertiary Care Centers
13.
Front Cell Infect Microbiol ; 10: 331, 2020.
Article in English | MEDLINE | ID: covidwho-634362

ABSTRACT

Objectives: Development and validation of a single-step and accurate reverse transcriptase loop-mediated isothermal amplification technique (RT-LAMP) for rapid identification of SARS-CoV-2 relative to commercial quantitative reverse transcriptase real-time PCR (qRT-PCR) assays to allow prompt initiation of proper medical care and containment of virus spread. Methods: Primers showing optimal in-silico features were subjected to analytical sensitivity and specificity to assess the limit of detection (LOD) and cross-reaction with closely- and distantly-related viral species, and clinically prominent bacterial and fungal species. In order to evaluate the clinical utility, our RT-LAMP was subjected to a large number of clinical samples, including 213 negative and 47 positive patients, relative to two commercial quantitative RT-PCR assays. Results: The analytical specificity and sensitivity of our assay was 100% and 500 copies/ml when serial dilution was performed in both water and sputum. Subjecting our RT-LAMP assay to clinical samples showed a high degree of specificity (99.5%), sensitivity (91.4%), positive predictive value (97.7%), and negative predictive value (98.1%) when used relative to qRT-PCR. Our RT-LAMP assay was two times faster than qRT-PCR and is storable at room temperature. A suspected case that later became positive tested positive using both our RT-LAMP and the two qRT-PCR assays, which shows the capability of our assay for screening purposes. Conclusions: We present a rapid RT-LAMP assay that could extend the capacity of laboratories to process two times more clinical samples relative to qRT-PCR and potentially could be used for high-throughput screening purposes when demand is increasing at critical situations.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Mass Screening/methods , Nucleic Acid Amplification Techniques , Pneumonia, Viral/diagnosis , Humans , Pandemics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
14.
Epidemiol Infect ; 148: e114, 2020 06 10.
Article in English | MEDLINE | ID: covidwho-624594

ABSTRACT

BACKGROUND: The median duration of hospital stays due to COVID-19 has been reported in several studies on China as 10-13 days. Global studies have indicated that the length of hospitalisation depends on different factors, such as the time elapsed from exposure to symptom onset, and from symptom onset to hospital admission, as well as specificities of the country under study. The goal of this paper is to identify factors associated with the median duration of hospital stays of COVID-19 patients during the second COVID-19 wave that hit Vietnam from 5 March to 8 April 2020. METHOD: We used retrospective data on 133 hospitalised patients with COVID-19 recorded over at least two weeks during the study period. The Cox proportional-hazards regression model was applied to determine the potential risk factors associated with length of hospital stay. RESULTS: There were 65 (48.9%) females, 98 (73.7%) patients 48 years old or younger, 15 (11.3%) persons with comorbidities, 21 (16.0%) severely ill patients and 5 (3.8%) individuals with life-threatening conditions. Eighty-two (61.7%) patients were discharged after testing negative for the SARS-CoV-2 virus, 51 were still in the hospital at the end of the study period and none died. The median duration of stay in a hospital was 21 (IQR: 16-34) days. The multivariable Cox regression model showed that age, residence and sources of contamination were significantly associated with longer duration of hospitalisation. CONCLUSION: A close look at how long COVID-19 patients stayed in the hospital could provide an overview of their treatment process in Vietnam, and support the country's National Steering Committee on COVID-19 Prevention and Control in the efficient allocation of resources over the next stages of the COVID-19 prevention period.


Subject(s)
Coronavirus Infections/epidemiology , Length of Stay/statistics & numerical data , Pneumonia, Viral/epidemiology , Quarantine/statistics & numerical data , Travel-Related Illness , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Betacoronavirus , Child , Child, Preschool , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Female , Geography , Hospitalization , Humans , Male , Middle Aged , Multivariate Analysis , Pandemics , Proportional Hazards Models , Real-Time Polymerase Chain Reaction , Residence Characteristics , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction , Risk Factors , Severity of Illness Index , Survival Analysis , Vietnam/epidemiology , Young Adult
15.
BMJ Case Rep ; 13(7)2020 Jul 01.
Article in English | MEDLINE | ID: covidwho-622599

ABSTRACT

Since December 2019, coronavirus disease 2019 (COVID-19) has been an international public health emergency. The possibility of COVID-19 should be considered primarily in patients with new-onset fever or respiratory tract symptoms. However, these symptoms can occur with other viral respiratory illnesses. We reported a case of severe acute respiratory syndrome coronavirus 2 and influenza A virus coinfection. During the epidemic, the possibility of COVID-19 should be considered regardless of positive findings for other pathogens.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Influenza A virus/isolation & purification , Influenza, Human/complications , Influenza, Human/diagnosis , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Amides/therapeutic use , Anti-Bacterial Agents/therapeutic use , Antiviral Agents/therapeutic use , Coinfection , Coronavirus Infections/drug therapy , Diagnosis, Differential , Glucocorticoids/therapeutic use , Humans , Influenza, Human/economics , Lung/diagnostic imaging , Male , Middle Aged , Pandemics , Pneumonia, Viral/drug therapy , Pregnenediones/therapeutic use , Pyrazines/therapeutic use , Radiography , Real-Time Polymerase Chain Reaction
16.
Medicine (Baltimore) ; 99(26): e20837, 2020 Jun 26.
Article in English | MEDLINE | ID: covidwho-616556

ABSTRACT

To compare clinical and imaging features between patients with an initial negative reverse-transcription-polymerase chain-reaction (RT-PCR) test and patients with an initial positive RT-PCR test. CT follow-up analysis in the negative RT-PCR group is also described.Thirty-three patients with SARS-CoV-2 infection confirmed by RT-PCR, with 216 lesions upon CT, were included. Demographic information and chest CT imaging features were collected.The average age in the whole study group was 46.9 ±â€Š11.1 years, with 18 males and 15 females. Patients in the positive RT-PCR test group were more likely to have a fever than patients in the negative RT-PCR test group (85.7% vs 50%, P < .05). Lesions in the positive group were more likely to be located in the peripheral area than lesions in the negative group (83.6% vs 68.2%, P < .05). Regarding the appearance of 216 lesions, ground-glass opacities (GGOs) with consolidation (43.2%) was the most common appearance in the negative group, followed by pure GGOs (31.8%), while in the positive group, pure GGOs (32%) and GGOs with interlobular septal thickening (32.8%) were both most frequent, and the difference between them was evident (P < .05). For the follow-up analysis, the largest short-axis of a lesion was smaller upon follow-up (median size 13.6 mm vs 14 mm), albeit by a smaller margin. Pure GGOs decreased in frequency, from 31.3% to 21.3%, while consolidation increased in frequency, from 7.5% to 12.5%.The manifestations of COVID-19 in patients with a first negative RT-PCR test and patients with a positive first RT-PCR test are different to some extent. The consolidation component may increase after follow-up.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Radiography, Thoracic/statistics & numerical data , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Adult , False Negative Reactions , Female , Humans , Male , Middle Aged , Pandemics , Retrospective Studies
17.
Eur Radiol Exp ; 4(1): 39, 2020 06 26.
Article in English | MEDLINE | ID: covidwho-615378

ABSTRACT

BACKGROUND: Computed tomography (CT) enables quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, helping in outcome prediction. METHODS: From 1 to 22 March 2020, patients with pneumonia symptoms, positive lung CT scan, and confirmed SARS-CoV-2 on reverse transcription-polymerase chain reaction (RT-PCR) were consecutively enrolled. Clinical data was collected. Outcome was defined as favourable or adverse (i.e., need for mechanical ventilation or death) and registered over a period of 10 days following CT. Volume of disease (VoD) on CT was calculated semi-automatically. Multiple linear regression was used to predict VoD by clinical/laboratory data. To predict outcome, important features were selected using a priori analysis and subsequently used to train 4 different models. RESULTS: A total of 106 consecutive patients were enrolled (median age 63.5 years, range 26-95 years; 41/106 women, 38.7%). Median duration of symptoms and C-reactive protein (CRP) was 5 days (range 1-30) and 4.94 mg/L (range 0.1-28.3), respectively. Median VoD was 249.5 cm3 (range 9.9-1505) and was predicted by lymphocyte percentage (p = 0.008) and CRP (p < 0.001). Important variables for outcome prediction included CRP (area under the curve [AUC] 0.77), VoD (AUC 0.75), age (AUC 0.72), lymphocyte percentage (AUC 0.70), coronary calcification (AUC 0.68), and presence of comorbidities (AUC 0.66). Support vector machine had the best performance in outcome prediction, yielding an AUC of 0.92. CONCLUSIONS: Measuring the VoD using a simple CT post-processing tool estimates SARS-CoV-2 burden. CT and clinical data together enable accurate prediction of short-term clinical outcome.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Lung/diagnostic imaging , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Tomography, X-Ray Computed/methods , Adult , Aged , Aged, 80 and over , Coronavirus Infections/diagnostic imaging , Evaluation Studies as Topic , Female , Humans , Male , Middle Aged , Pandemics , Patient Outcome Assessment , Pneumonia, Viral/diagnostic imaging , Predictive Value of Tests , Prognosis , Reproducibility of Results
18.
Ann Agric Environ Med ; 27(2): 317-318, 2020 Jun 19.
Article in English | MEDLINE | ID: covidwho-614679

ABSTRACT

INTRODUCTION: Diagnostic procedure in Coronavirus Disease 2019 (COVID-19) is based mainly on performing real-time-reverse transcription-polymerase chain-reaction (RT-PCR), which has been accepted as the gold standard method. In some cases, such as mutations of the SARS-CoV-2 genome, variable viral load kinetics or laboratory errors, it can be false-negative. CASE REPORT: The case is presented of a 56-year-old man with respiratory tract symptoms, with twice negative results of real-time-reverse transcription-polymerase chain-reaction of nasopharyngeal swabs and positive chest computed tomography, with typical findings for COVID-19 pneumonia. CONCLUSIONS: Patients with negative RT-PCR results, but with positive computed tomography findings characteristic for COVID-19, should be treated as well as those infected.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Coronavirus Infections/pathology , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/pathology , Humans , Male , Middle Aged , Pandemics , Radiography, Thoracic , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Tomography, X-Ray Computed
19.
Viruses ; 12(6)2020 06 25.
Article in English | MEDLINE | ID: covidwho-613542

ABSTRACT

The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide has highlighted the importance of reliable and rapid diagnostic testing to prevent and control virus circulation. Dozens of monoplex in-house RT-qPCR assays are already available; however, the development of dual-target assays is suited to avoid false-negative results caused by polymorphisms or point mutations, that can compromise the accuracy of diagnostic and screening tests. In this study, two mono-target assays recommended by WHO (E-Sarbeco (enveloppe gene, Charite University, Berlin, Germany) and RdRp-IP4 (RdRp, Institut Pasteur, Paris, France)) were selected and combined in a unique robust test; the resulting duo SARS-CoV-2 RT-qPCR assay was compared to the two parental monoplex tests. The duo SARS-CoV-2 assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. We demonstrated that combining two single systems into a dual-target assay (with or without an MS2-based internal control) did not impair performances, providing a potent tool adapted for routine molecular diagnosis in clinical microbiology laboratories.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA Replicase/genetics , Real-Time Polymerase Chain Reaction/methods , Viral Envelope Proteins/genetics , Viral Nonstructural Proteins/genetics , Betacoronavirus/genetics , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/virology , RNA, Viral/analysis , Sensitivity and Specificity , World Health Organization
20.
Clin Gastroenterol Hepatol ; 18(8): 1753-1759.e2, 2020 07.
Article in English | MEDLINE | ID: covidwho-613156

ABSTRACT

BACKGROUND & AIMS: We compared clinical, laboratory, radiological, and outcome features of patients with SARS-CoV-2 infection (COVID-19) with pneumonia, with vs without diarrhea. METHODS: We performed a retrospective, single-center analysis of 84 patients with SARS-CoV-2 pneumonia in Wuhan Union Hospital, China, from January 19 through February 7, 2020. Cases were confirmed by real-time reverse-transcriptase PCR of nasal and pharyngeal swab specimens for SARS-CoV-2 RNA. Blood samples were analyzed for white blood cell count, lymphocyte count, alanine aminotransferase, creatine kinase, lactate dehydrogenase, D-dimer, C-reactive protein, and in some cases, immunoglobulins, complement, lymphocyte subsets, and cytokines. Virus RNA was detected in stool samples by real-time PCR. RESULTS: Of the 84 patients with SARS-CoV-2 pneumonia, 26 (31%) had diarrhea. The duration of fever and dyspnea in patients with diarrhea was significantly longer than those without diarrhea (all P < .05). Stool samples from a higher proportion of patients with diarrhea tested positive for virus RNA (69%) than from patients without diarrhea (17%) (P < .001). As of February 19, a lower proportion of patients with diarrhea had a negative result from the latest throat swab for SARS-CoV-2 (77%) than patients without diarrhea (97%) (P = .010), during these patients' hospitalization. Of 76 patients with a negative result from their latest throat swab test during hospitalization, a significantly higher proportion of patients with diarrhea had a positive result from the retest for SARS-CoV-2 in stool (45%) than patients without diarrhea (20%) (P = .039). CONCLUSIONS: At a single center in Wuhan, China, 31% of patients with SARS-CoV-2 pneumonia had diarrhea. A significantly higher proportion of patients with diarrhea have virus RNA in stool than patients without diarrhea. Elimination of SARS-CoV-2 from stool takes longer than elimination from the nose and throat.


Subject(s)
Betacoronavirus/isolation & purification , Carrier State/virology , Coronavirus Infections/complications , Coronavirus Infections/pathology , Diarrhea/epidemiology , Diarrhea/etiology , Pneumonia, Viral/complications , Pneumonia, Viral/pathology , Adult , Aged , Blood Cell Count , Blood Chemical Analysis , China , Diarrhea/pathology , Feces/virology , Female , Hospitals , Humans , Male , Middle Aged , Nasal Mucosa/virology , Pandemics , Pharynx/virology , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Retrospective Studies , Young Adult
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