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1.
Nat Biotechnol ; 38(8): 970-979, 2020 08.
Article in English | MEDLINE | ID: covidwho-616612

ABSTRACT

To investigate the immune response and mechanisms associated with severe coronavirus disease 2019 (COVID-19), we performed single-cell RNA sequencing on nasopharyngeal and bronchial samples from 19 clinically well-characterized patients with moderate or critical disease and from five healthy controls. We identified airway epithelial cell types and states vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In patients with COVID-19, epithelial cells showed an average three-fold increase in expression of the SARS-CoV-2 entry receptor ACE2, which correlated with interferon signals by immune cells. Compared to moderate cases, critical cases exhibited stronger interactions between epithelial and immune cells, as indicated by ligand-receptor expression profiles, and activated immune cells, including inflammatory macrophages expressing CCL2, CCL3, CCL20, CXCL1, CXCL3, CXCL10, IL8, IL1B and TNF. The transcriptional differences in critical cases compared to moderate cases likely contribute to clinical observations of heightened inflammatory tissue damage, lung injury and respiratory failure. Our data suggest that pharmacologic inhibition of the CCR1 and/or CCR5 pathways might suppress immune hyperactivation in critical COVID-19.


Subject(s)
Coronavirus Infections/pathology , Coronavirus Infections/physiopathology , Pneumonia, Viral/pathology , Pneumonia, Viral/physiopathology , Respiratory System/pathology , Single-Cell Analysis , Transcriptome , Adult , Aged , Bronchoalveolar Lavage Fluid/virology , Cell Communication , Cell Differentiation , Coronavirus Infections/virology , Epithelial Cells/pathology , Epithelial Cells/virology , Female , Humans , Immune System/pathology , Inflammation/immunology , Inflammation/pathology , Longitudinal Studies , Male , Middle Aged , Nasopharynx/virology , Pandemics , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/virology , Respiratory System/immunology , Respiratory System/virology , Severity of Illness Index
2.
J Popul Ther Clin Pharmacol ; 27(S Pt 1): e5-e10, 2020 06 03.
Article in English | MEDLINE | ID: covidwho-602504

ABSTRACT

The COVID-19 virus has spread rapidly around the world and there are many patients in multiple countries. Great efforts have been made to find effective medications against the COVID-19. This study aims to compare the effectiveness of LINCOCIN® and AZITRO® in the treatment of COVID-19 associated pneumonia. A total of 24 hospitalized patients aged between 30-80 years who were admitted to the Tarsus Medical Park Hospital between February to March 2020 was included in the study. The patients were divided into LINCOCIN® and AZITRO® treatment groups. Bronchoalveolar-lavage PCR results were compared after treatment. The mean age was 58.4±15.4 years in the LINCOCIN® group and 59.1±16.6 years in the AZITRO® group. In the LINCOCIN® group, the rate of males was 66.7% and it was 58.3% in the AZITRO® group. There were no statistical differences in terms of age and gender between the groups. On the 6th day after starting treatment, negative bronchoalveolar PCR result was 83.3% in the LINCOCIN® group and 33.3% in the AZITRO® group. The negative bronchoalveolar PCR proportion was significantly higher in the LINCOCIN® group than in the AZITRO® group. LINCOCIN® usage may be more appropriate in the treatment of COVID-19 associated pneumonia. Further studies with a large sample size should clarify these results.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Azithromycin/therapeutic use , Coronavirus Infections/complications , Lincomycin/therapeutic use , Pneumonia, Viral/drug therapy , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/adverse effects , Azithromycin/administration & dosage , Azithromycin/adverse effects , Betacoronavirus , Bronchoalveolar Lavage Fluid/virology , Female , Humans , Lincomycin/administration & dosage , Lincomycin/adverse effects , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/etiology , Pneumonia, Viral/virology , Prospective Studies , Risk Factors
3.
J Popul Ther Clin Pharmacol ; 27(S Pt 1): e5-e10, 2020 06 03.
Article in English | MEDLINE | ID: covidwho-601932

ABSTRACT

The COVID-19 virus has spread rapidly around the world and there are many patients in multiple countries. Great efforts have been made to find effective medications against the COVID-19. This study aims to compare the effectiveness of LINCOCIN® and AZITRO® in the treatment of COVID-19 associated pneumonia. A total of 24 hospitalized patients aged between 30-80 years who were admitted to the Tarsus Medical Park Hospital between February to March 2020 was included in the study. The patients were divided into LINCOCIN® and AZITRO® treatment groups. Bronchoalveolar-lavage PCR results were compared after treatment. The mean age was 58.4±15.4 years in the LINCOCIN® group and 59.1±16.6 years in the AZITRO® group. In the LINCOCIN® group, the rate of males was 66.7% and it was 58.3% in the AZITRO® group. There were no statistical differences in terms of age and gender between the groups. On the 6th day after starting treatment, negative bronchoalveolar PCR result was 83.3% in the LINCOCIN® group and 33.3% in the AZITRO® group. The negative bronchoalveolar PCR proportion was significantly higher in the LINCOCIN® group than in the AZITRO® group. LINCOCIN® usage may be more appropriate in the treatment of COVID-19 associated pneumonia. Further studies with a large sample size should clarify these results.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Azithromycin/therapeutic use , Coronavirus Infections/complications , Lincomycin/therapeutic use , Pneumonia, Viral/drug therapy , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/administration & dosage , Anti-Bacterial Agents/adverse effects , Azithromycin/administration & dosage , Azithromycin/adverse effects , Betacoronavirus , Bronchoalveolar Lavage Fluid/virology , Female , Humans , Lincomycin/administration & dosage , Lincomycin/adverse effects , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/etiology , Pneumonia, Viral/virology , Prospective Studies , Risk Factors
4.
Eur Rev Med Pharmacol Sci ; 24(10): 5830-5841, 2020 May.
Article in English | MEDLINE | ID: covidwho-547471

ABSTRACT

OBJECTIVE: Recent worldwide outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of respiratory coronavirus disease 2019 (COVID-19), is a current, ongoing life-threatening crisis, and international public health emergency. The early diagnosis and management of the disease remains a major challenge. In this review, we aim to summarize the updated epidemiology, causes, clinical manifestation and diagnosis, as well as prevention and control of the novel coronavirus SARS-CoV-2. MATERIALS AND METHODS: A broad search of the literature was performed in "PubMed" "Medline" "Web of Science", "Google Scholar" and "World Health Organization-WHO" using the keywords "severe acute respiratory syndrome coronavirus", "2019-nCoV", "COVID-19, "SARS", "SARS-CoV-2" "Epidemiology" "Transmission" "Pathogenesis" "Clinical Characteristics". We reviewed and documented the information obtained from literature on epidemiology, pathogenesis and clinical appearances of SARS-CoV-2 infection. RESULTS: The global cases of COVID-19 as of April 2, 2020, have risen to more than 900,000 and morbidity has reached more than 47,000. The incidence rate for COVID-19 has been predicted to be higher than the previous outbreaks of other coronavirus family members, including those of SARS-CoV and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The main clinical presentation of SARS-CoV-2 infection ranges from asymptomatic stages to severe lower respiratory infection in the form of pneumonia. Most of the patients also presented with fever, cough, sore throat, headache, fatigue, myalgia and breathlessness. Individuals at higher risk for severe illness include elderly people and patients with a weakened immune system or that are suffering from an underlying chronic medical condition like hypertension, diabetes mellitus, cancer, respiratory illness or cardiovascular diseases. CONCLUSIONS: SARS-Cov-2 has emerged as a worldwide threat, currently affecting 170 countries and territories across the globe. There is still much to be understood regarding SARS-CoV-2 about its virology, epidemiology and clinical management strategies; this knowledge will be essential to both manage the current pandemic and to conceive comprehensive measures to prevent such outbreaks in the future.


Subject(s)
Betacoronavirus/physiology , Coronavirus Infections/pathology , Pneumonia, Viral/pathology , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Bronchoalveolar Lavage Fluid/virology , Comorbidity , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Humans , Lung Neoplasms/complications , Lung Neoplasms/pathology , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Quarantine , RNA, Viral/genetics , RNA, Viral/metabolism , Sputum/virology
5.
Mycoses ; 63(6): 528-534, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-547397

ABSTRACT

OBJECTIVES: Patients with acute respiratory distress syndrome (ARDS) due to viral infection are at risk for secondary complications like invasive aspergillosis. Our study evaluates coronavirus disease 19 (COVID-19) associated invasive aspergillosis at a single centre in Cologne, Germany. METHODS: A retrospective chart review of all patients with COVID-19 associated ARDS admitted to the medical or surgical intensive care unit at the University Hospital of Cologne, Cologne, Germany. RESULTS: COVID-19 associated invasive pulmonary aspergillosis was found in five of 19 consecutive critically ill patients with moderate to severe ARDS. CONCLUSION: Clinicians caring for patients with ARDS due to COVID-19 should consider invasive pulmonary aspergillosis and subject respiratory samples to comprehensive analysis to detect co-infection.


Subject(s)
Coronavirus Infections/complications , Pneumonia, Viral/complications , Pulmonary Aspergillosis/complications , Respiratory Distress Syndrome, Adult/complications , Aged , Antifungal Agents/therapeutic use , Bronchoalveolar Lavage Fluid/chemistry , Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/diagnostic imaging , Female , Germany , Hemorrhage/etiology , Hospitals, Teaching , Humans , Intensive Care Units , Lung Diseases/etiology , Male , Mannans/analysis , Metapneumovirus/isolation & purification , Middle Aged , Nitriles/therapeutic use , Pandemics , Paramyxoviridae Infections/etiology , Pneumonia, Viral/diagnostic imaging , Pulmonary Aspergillosis/diagnostic imaging , Pyridines/therapeutic use , Respiratory Distress Syndrome, Adult/diagnostic imaging , Retrospective Studies , Thorax/diagnostic imaging , Tomography, X-Ray Computed , Triazoles/therapeutic use , Voriconazole/therapeutic use
6.
Sci Adv ; 6(25): eabb5813, 2020 06.
Article in English | MEDLINE | ID: covidwho-619103

ABSTRACT

The COVID-19 outbreak has become a global health risk, and understanding the response of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host deaminases is an innate restriction process to counter virus infection, but it is not yet known whether this process operates against coronaviruses. Here, we analyze RNA sequences from bronchoalveolar lavage fluids obtained from coronavirus-infected patients. We identify nucleotide changes that may be signatures of RNA editing: adenosine-to-inosine changes from ADAR deaminases and cytosine-to-uracil changes from APOBEC deaminases. Mutational analysis of genomes from different strains of Coronaviridae from human hosts reveals mutational patterns consistent with those observed in the transcriptomic data. However, the reduced ADAR signature in these data raises the possibility that ADARs might be more effective than APOBECs in restricting viral propagation. Our results thus suggest that both APOBECs and ADARs are involved in coronavirus genome editing, a process that may shape the fate of both virus and patient.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/metabolism , Coronavirus Infections/genetics , Host-Pathogen Interactions/genetics , Pneumonia, Viral/genetics , RNA Editing/genetics , Transcriptome , APOBEC Deaminases/genetics , APOBEC Deaminases/metabolism , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , Base Sequence/genetics , Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/virology , Genome, Viral/genetics , Humans , Mutation Rate , Nucleotides/genetics , Nucleotides/metabolism , Pandemics , Pneumonia, Viral/virology , RNA, Viral/genetics , Virus Replication/genetics
7.
Emerg Infect Dis ; 26(8): 1842-1845, 2020 08.
Article in English | MEDLINE | ID: covidwho-403054

ABSTRACT

We report phylogenetic and mutational analysis of severe acute respiratory syndrome coronavirus 2 virus strains from the Lazio region of Italy and provide information about the dynamics of virus spread. Data suggest effective containment of clade V strains, but subsequently, multiple waves of clade G strains were circulating widely in Europe.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , RNA, Viral/genetics , Adult , Aged , Betacoronavirus/classification , Betacoronavirus/pathogenicity , Bronchoalveolar Lavage Fluid/virology , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Female , High-Throughput Nucleotide Sequencing , Hospitalization , Humans , Italy/epidemiology , Male , Middle Aged , Mutation , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Prospective Studies , Real-Time Polymerase Chain Reaction , Severity of Illness Index , Time Factors
8.
Science ; 369(6505): 812-817, 2020 08 14.
Article in English | MEDLINE | ID: covidwho-327276

ABSTRACT

An understanding of protective immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for vaccine and public health strategies aimed at ending the global coronavirus disease 2019 (COVID-19) pandemic. A key unanswered question is whether infection with SARS-CoV-2 results in protective immunity against reexposure. We developed a rhesus macaque model of SARS-CoV-2 infection and observed that macaques had high viral loads in the upper and lower respiratory tract, humoral and cellular immune responses, and pathologic evidence of viral pneumonia. After the initial viral clearance, animals were rechallenged with SARS-CoV-2 and showed 5 log10 reductions in median viral loads in bronchoalveolar lavage and nasal mucosa compared with after the primary infection. Anamnestic immune responses after rechallenge suggested that protection was mediated by immunologic control. These data show that SARS-CoV-2 infection induced protective immunity against reexposure in nonhuman primates.


Subject(s)
Betacoronavirus , Coronavirus Infections/immunology , Pneumonia, Viral/immunology , Animals , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Betacoronavirus/immunology , Betacoronavirus/physiology , Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Disease Models, Animal , Female , Immunity, Cellular , Immunity, Humoral , Immunologic Memory , Lung/immunology , Lung/pathology , Lung/virology , Lung Diseases, Interstitial/immunology , Lung Diseases, Interstitial/pathology , Lung Diseases, Interstitial/virology , Macaca mulatta , Male , Nasal Mucosa/virology , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Recurrence , Spike Glycoprotein, Coronavirus/immunology , Viral Load , Virus Replication
9.
Science ; 369(6505): 806-811, 2020 08 14.
Article in English | MEDLINE | ID: covidwho-326877

ABSTRACT

The global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made the development of a vaccine a top biomedical priority. In this study, we developed a series of DNA vaccine candidates expressing different forms of the SARS-CoV-2 spike (S) protein and evaluated them in 35 rhesus macaques. Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers at levels comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. After vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log10 reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with viral loads in sham controls. Vaccine-elicited neutralizing antibody titers correlated with protective efficacy, suggesting an immune correlate of protection. These data demonstrate vaccine protection against SARS-CoV-2 in nonhuman primates.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Spike Glycoprotein, Coronavirus/immunology , Vaccines, DNA/immunology , Viral Vaccines/immunology , Adjuvants, Immunologic , Animals , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Betacoronavirus/physiology , Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Disease Models, Animal , Female , Humans , Immunity, Cellular , Immunity, Humoral , Immunization, Secondary , Immunogenicity, Vaccine , Immunologic Memory , Macaca mulatta , Male , Mutant Proteins/chemistry , Mutant Proteins/immunology , Nasal Mucosa/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Protein Domains , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Vaccination , Vaccines, DNA/administration & dosage , Viral Load , Viral Vaccines/administration & dosage
10.
Nat Med ; 26(6): 842-844, 2020 06.
Article in English | MEDLINE | ID: covidwho-244490

ABSTRACT

Respiratory immune characteristics associated with Coronavirus Disease 2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid immune cells from patients with varying severity of COVID-19 and from healthy people by using single-cell RNA sequencing. Proinflammatory monocyte-derived macrophages were abundant in the bronchoalveolar lavage fluid from patients with severe COVID-9. Moderate cases were characterized by the presence of highly clonally expanded CD8+ T cells. This atlas of the bronchoalveolar immune microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/immunology , Coronavirus Infections/pathology , Pneumonia, Viral/immunology , Pneumonia, Viral/pathology , Single-Cell Analysis , Bronchoalveolar Lavage Fluid/immunology , Bronchoalveolar Lavage Fluid/virology , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/virology , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Humans , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology
13.
BMC Infect Dis ; 20(1): 317, 2020 Apr 30.
Article in English | MEDLINE | ID: covidwho-144086

ABSTRACT

BACKGROUND: The novel coronavirus disease 2019 (COVID-19) outbreak started in Wuhan, Hubei, China since Dec 2019 and cases of infection have been continuously reported in various countries. It is now clear that the SARS-COV-2 coronavirus is transmissible from human to human. Nucleic acid detection is considered as the gold standard for the diagnosis of COVID-19. In this case report, we describe our experience in detection of SARS-COV-2 from a confirmed patient using nucleic acid test of bronchoalveolar-lavage fluid (BALF) samples but not nasopharyngeal swabs. CASE PRESENTATION: We present a case of severely ill SARS-COV-2 infected 46-year-old man with fever, coughing and chest tightness. We performed viral detection using his BALF samples and imaging method (CT) for confirmation. The patient received combination of interferonalfa-1b and ribavirin, lopinavir and ritonavir for antiviral treatment at different stages. Other medication was also given to him in combination for anti-inflammation, intestinal microbial regulation, phlegm elimination, liver protection and pulmonary fibrosis prevention purposes. We provided oxygen supply to him using BIPAP ventilator and high-flow humidification oxygen therapy instrument to facilitate respiration. The patient was cured and discharged. CONCLUSION: This case report described an effective supportive medication scheme to treat SARS-COV-2 infected patient and emphasized the necessity of detection of the viral genome using BALF samples and its significance in the diagnosis and prognosis of the disease.


Subject(s)
Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Antiviral Agents/therapeutic use , Betacoronavirus , China , Coronavirus Infections/drug therapy , Cough/etiology , Fever/etiology , Humans , Lung/diagnostic imaging , Male , Middle Aged , Nasopharynx/virology , Pandemics , Pneumonia, Viral/drug therapy
14.
J Clin Virol ; 127: 104384, 2020 06.
Article in English | MEDLINE | ID: covidwho-125163

ABSTRACT

In December 2019, a novel coronavirus (SARS-CoV-2) was first isolated from Wuhan city, China and within three months, the global community was challenged with a devastating pandemic. The rapid spread of the virus challenged diagnostic laboratories to rapidly develop molecular diagnostic methods. As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. This study compares the validation of three different molecular assays at the Johns Hopkins Molecular Virology laboratory: the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. Overall, our studies indicate a comparable analytical performance of the three assays for the detection of SARS-CoV-2.


Subject(s)
Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Reagent Kits, Diagnostic/standards , Betacoronavirus/isolation & purification , Bronchoalveolar Lavage Fluid/virology , Humans , Molecular Diagnostic Techniques/standards , Nasopharynx/virology , Pandemics , Sensitivity and Specificity
15.
Mycoses ; 63(6): 528-534, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-125102

ABSTRACT

OBJECTIVES: Patients with acute respiratory distress syndrome (ARDS) due to viral infection are at risk for secondary complications like invasive aspergillosis. Our study evaluates coronavirus disease 19 (COVID-19) associated invasive aspergillosis at a single centre in Cologne, Germany. METHODS: A retrospective chart review of all patients with COVID-19 associated ARDS admitted to the medical or surgical intensive care unit at the University Hospital of Cologne, Cologne, Germany. RESULTS: COVID-19 associated invasive pulmonary aspergillosis was found in five of 19 consecutive critically ill patients with moderate to severe ARDS. CONCLUSION: Clinicians caring for patients with ARDS due to COVID-19 should consider invasive pulmonary aspergillosis and subject respiratory samples to comprehensive analysis to detect co-infection.


Subject(s)
Coronavirus Infections/complications , Pneumonia, Viral/complications , Pulmonary Aspergillosis/complications , Respiratory Distress Syndrome, Adult/complications , Aged , Antifungal Agents/therapeutic use , Bronchoalveolar Lavage Fluid/chemistry , Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/diagnostic imaging , Female , Germany , Hemorrhage/etiology , Hospitals, Teaching , Humans , Intensive Care Units , Lung Diseases/etiology , Male , Mannans/analysis , Metapneumovirus/isolation & purification , Middle Aged , Nitriles/therapeutic use , Pandemics , Paramyxoviridae Infections/etiology , Pneumonia, Viral/diagnostic imaging , Pulmonary Aspergillosis/diagnostic imaging , Pyridines/therapeutic use , Respiratory Distress Syndrome, Adult/diagnostic imaging , Retrospective Studies , Thorax/diagnostic imaging , Tomography, X-Ray Computed , Triazoles/therapeutic use , Voriconazole/therapeutic use
16.
J Clin Virol ; 127: 104381, 2020 06.
Article in English | MEDLINE | ID: covidwho-102384

ABSTRACT

BACKGROUND: A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in China in late 2019 and subsequently caused a pandemic. Surveillance is important to better appreciate this evolving pandemic and to longitudinally monitor the effectiveness of public health measures. OBJECTIVES: We aimed to provide a rapid, easy to establish and costeffective laboratory-based surveillance tool for SARS-CoV-2. STUDY DESIGN: We used minipools of RNA prepared from nucleic acid extractions of routine respiratory samples. We technically validated the assay and distributed the protocol within an informal network of five German university laboratories. RESULTS: We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany from 17.02.2020 to 10.03.2020. One minipool reacted positive and after resolution one individual sample tested SARS-CoV-2 positive. This sample was from a hospitalized patient not suspected of having contracted SARS-CoV-2. CONCLUSIONS: Our approach of a laboratory-based surveillance for SARSCoV-2 using minipools proved its concept is easily adaptable and resource-saving. It might assist not only public health laboratories in SARS-CoV-2 surveillance.


Subject(s)
Coronavirus Infections/diagnosis , Epidemiological Monitoring , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction , Betacoronavirus/isolation & purification , Bronchoalveolar Lavage Fluid/virology , Germany/epidemiology , Humans , Pandemics , Pharynx/virology , Prospective Studies , Sputum/virology
17.
Zhonghua Jie He He Hu Xi Za Zhi ; 43(4): 337-339, 2020 Apr 12.
Article in Chinese | MEDLINE | ID: covidwho-72739

ABSTRACT

The case reports 2 cases of novel coronavirus pneumonia diagnosed by concurrent bronchoalveolar lavage in our hospital, 1 case had a history of epidemiology, clinical symptoms and high imaging suspicion, but repeated negative throat swabs. One patient was diagnosed 2019-nCoV. Before the patient was discharged, the clinical symptoms disappeared, the chest CT showed significant improvement, and the pharynx swab was twice negative, reaching the discharge standard.We detected the ORF 1ab gene, the N gene and the nucleic acid of the new coronavirus in the broncho-alveolar lavage fluid of 2 patients. The results showed that the positive rate of bronchoalveolar lavage for detection of new coronavirus nucleic acid was high, and bronchoalveolar lavage for suspected or confirmed new coronavirus pneumonia patients with negative detection of nucleic acid in pharynx swabs but still residual lung lesions was helpful for early diagnosis, treatment and prognosis.


Subject(s)
Bronchoalveolar Lavage Fluid/virology , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus , Bronchoalveolar Lavage , Clinical Laboratory Techniques , Genes, Viral , Humans , Pandemics , Pharynx/virology
18.
Emerg Infect Dis ; 26(6): 1324-1326, 2020 06.
Article in English | MEDLINE | ID: covidwho-6800

ABSTRACT

We report co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus in a patient with pneumonia in China. The case highlights possible co-detection of known respiratory viruses. We noted low sensitivity of upper respiratory specimens for SARS-CoV-2, which could further complicate recognition of the full extent of disease.


Subject(s)
Coronavirus Infections/diagnosis , Influenza, Human/diagnosis , Pneumonia, Viral/diagnosis , Aged , Betacoronavirus/isolation & purification , Bronchoalveolar Lavage Fluid/virology , China , Clinical Laboratory Techniques , Coinfection , Coronavirus Infections/virology , Humans , Influenza A virus , Influenza, Human/virology , Male , Nasopharynx/virology , Pandemics , Pneumonia, Viral/virology
19.
Clin Chim Acta ; 505: 172-175, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-5447

ABSTRACT

BACKGROUND: There's an outbreak of a novel coronavirus (SARS-CoV-2) infection since December 2019, first in China, and currently with more than 80 thousand confirmed infection globally in 29 countries till March 2, 2020. Identification, isolation and caring for patients early are essential to limit human-to-human transmission including reducing secondary infections among close contacts and health care workers, preventing transmission amplification events. The RT-PCR detection of viral nucleic acid test (NAT) was one of the most quickly established laboratory diagnosis method in a novel viral pandemic, just as in this COVID-19 outbreak. METHODS: 4880 cases that had respiratory infection symptoms or close contact with COVID-19 patients in hospital in Wuhan, China, were tested for SARS-CoV-2 infection by use of quantitative RT-PCR (qRT-PCR) on samples from the respiratory tract. Positive rates were calculated in groups divided by genders or ages. RESULTS: The positive rate was about 38% for the total 4880 specimens. Male and older population had a significant higher positive rates. However, 57% was positive among the specimens from the Fever Clinics. Binary logistic regression analysis showed that age, not gender, was the risk factor for SARS-CoV-2 infection in fever clinics. CONCLUSIONS: Therefore, we concluded that viral NAT played an important role in identifying SARS-CoV-2 infection.


Subject(s)
Betacoronavirus/chemistry , Coronavirus Infections/diagnosis , DNA, Viral/analysis , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Adolescent , Adult , Age Factors , Aged , Bronchoalveolar Lavage Fluid/virology , China/epidemiology , Clinical Laboratory Techniques , Coronavirus Infections/epidemiology , Disease Outbreaks , Female , Humans , Male , Middle Aged , Nucleocapsid/chemistry , Nucleocapsid/genetics , Pandemics , Pneumonia, Viral/epidemiology , Respiratory System/virology , Risk Factors , Sex Factors , Sputum/virology , Young Adult
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