Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 25
Filter
1.
Int J Infect Dis ; 108: 187-189, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1351682

ABSTRACT

OBJECTIVES: The present study compared the performance of the Lumipulse G Sars-CoV-2 Ag kit with the TaqPath COVID-19 RT-PCR CE IVD kit. METHODS: The study was conducted on 4266 naso-oropharyngeal swabs. Samples were subjected to antigen RT-PCR tests for the detection of Sars-CoV-2 and related variants. Statistical analyses were conducted in R software. RESULTS: We found 503 positives (including 138 H69-V70 deletion carriers) and 3763 negatives by RT-PCR, whereas 538 positives and 3728 negatives were obtained by antigen testing. We achieved empirical and binormal AU-ROCs of 0.920 and 0.990, accuracy of 0.960, sensitivity of 0.866, specificity of 0.973, positive and negative predictive values of 0.810 and 0.980. We obtained a positive correlation between viral loads and antigen levels (R2 = 0.81), finding a complete concordance for high viral loads (log10 copies/mL > 5.4). Antigen levels > 222 pg/mL were found to be reliable in assigning positive samples (p < 0.01). Concerning variant carriers, antigen test detected them with the same accuracy as other positive samples. CONCLUSIONS: Molecular and antigen tests should be evaluated regarding the prevalence of the area. In case of low prevalence, antigen testing can be employed as a first-line screening for the timely identification of affected individuals with high viral load, also if carriers of Sars-CoV-2 variants.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Sensitivity and Specificity , Viral Load
2.
J Med Virol ; 93(7): 4392-4398, 2021 07.
Article in English | MEDLINE | ID: covidwho-1263103

ABSTRACT

With the arrival of coronavirus disease 2019 (COVID-19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV-C), Enterovirus 68 (EV-68), and rhinovirus (RV) besides SARS-CoV-2 among hospitalized patients suspect of COVID-19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in respiratory samples using naso-oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS-CoV-2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV-68, 67 (6.78%) samples were positive for HAdV-C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS-CoV-2, FLUAV, and HAdV-C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID-19 and the high influenza vaccination coverage in the region in which this study was performed.


Subject(s)
Adenoviridae Infections/epidemiology , COVID-19/epidemiology , Common Cold/epidemiology , Enterovirus Infections/epidemiology , Influenza, Human/epidemiology , Physical Distancing , Adenoviridae Infections/prevention & control , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/prevention & control , Child , Child, Preschool , Coinfection/epidemiology , Coinfection/virology , Common Cold/prevention & control , Enterovirus D, Human/genetics , Enterovirus D, Human/isolation & purification , Enterovirus Infections/prevention & control , Female , Humans , Infant , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/prevention & control , Male , Masks , Mastadenovirus/genetics , Mastadenovirus/isolation & purification , Middle Aged , Nucleic Acid Amplification Techniques/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
3.
Am J Infect Control ; 49(9): 1165-1176, 2021 09.
Article in English | MEDLINE | ID: covidwho-1152221

ABSTRACT

OBJECTIVE: The COVID-19 pandemic raises an urgent need for large-scale control through easier, cheaper, and safer diagnostic specimens, including saliva and sputum. We aimed to conduct a systemic review and meta-analysis on the reliability and sensitivity of SARS-CoV-2 detection in saliva and deep throat sputum (DTS) compared to nasopharyngeal, combined naso/oropharyngeal, and oropharyngeal swabs. METHODS: This systematic review and meta-analysis was performed according to the PRISMA statement. The inclusion criteria were studies that specifically assessed a sample of saliva or DTS with at least one other respiratory specimen in patients with COVID-19 infection, based on RT-PCR tests. The DerSimonian-Laird bivariate random-effects model analysis performed using STATA software with the "metaprop" package. RESULTS: From 1598 studies, we retrieved 33 records, of which 26 studies were included for quantitative analysis. We found an overall sensitivity of 97% (95% confidence interval [CI], 86-100) for bronchoalveolar lavage fluid, 92% (95% CI, 80-99) for double naso/oropharyngeal swabs, 87% (95% CI, 77-95) for nasopharyngeal swabs, 83% (95% CI, 77-89) for saliva, 82% (95% CI, 76-88) for DTS, and 44% (95% CI, 35-52) for oropharyngeal swabs among symptomatic patients, respectively. Regardless of the type of specimens, the viral load and sensitivity in the severe patients were higher than mild and in the symptomatic patients higher than asymptomatic cases. CONCLUSIONS: The present review provides evidence for the diagnostic value of different respiratory specimens and supports saliva and DTS as promising diagnostic tools for first-line screening of SARS-CoV-2 infection. However, the methods of sampling, storing, and laboratory assay need to be optimized and validated before introducing as a definitive diagnosis tool. Saliva, DTS, and nasopharyngeal swab showed approximately similar results, and sensitivity was directly related to the disease severity. This review revealed a relationship between viral load, disease severity, and test sensitivity. None of the specimens showed appropriate diagnostic sensitivity for asymptomatic patients.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Nasopharynx , Pandemics , Pharynx , Reproducibility of Results , Saliva , Specimen Handling , Sputum
4.
PLoS Pathog ; 17(3): e1009374, 2021 03.
Article in English | MEDLINE | ID: covidwho-1143300

ABSTRACT

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T ('Basel cluster'), including 157 identical sequences at the root of the 'Basel cluster', some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions. Trial Registration: ClinicalTrials.gov NCT04351503.


Subject(s)
COVID-19/diagnosis , Contact Tracing/methods , Crowding , Genome, Viral , Mutation , SARS-CoV-2/genetics , Adult , COVID-19/epidemiology , COVID-19/genetics , Female , Humans , Longitudinal Studies , Male , Mass Screening , Middle Aged , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Switzerland/epidemiology
5.
Nat Commun ; 12(1): 1660, 2021 03 12.
Article in English | MEDLINE | ID: covidwho-1132065

ABSTRACT

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.


Subject(s)
COVID-19/genetics , COVID-19/virology , SARS-CoV-2/genetics , Adult , Aged , Angiotensin Receptor Antagonists/pharmacology , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antiviral Agents/pharmacology , COVID-19/drug therapy , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing , Drug Interactions , Female , Gene Expression Profiling , Genome, Viral , HLA Antigens/genetics , Host Microbial Interactions/drug effects , Host Microbial Interactions/genetics , Humans , Male , Middle Aged , Molecular Diagnostic Techniques , New York City/epidemiology , Nucleic Acid Amplification Techniques , Pandemics , RNA-Seq , SARS-CoV-2/classification , SARS-CoV-2/drug effects
6.
Fam Pract ; 38(5): 598-605, 2021 09 25.
Article in English | MEDLINE | ID: covidwho-1122622

ABSTRACT

BACKGROUND AND OBJECTIVES: Rapid multi-viral respiratory microbiological point-of-care tests (POCTs) have not been evaluated in UK primary care. The aim of this study was to evaluate the use of a multi-viral microbiological POCT for suspected respiratory tract infections (RTIs). METHODS: In this observational, mixed-methods feasibility study practices were provided with a POCT machine for any patient aged ≥3 months with suspected RTI. Dual throat/nose swabs tested for 17 respiratory viruses and three atypical bacteria, 65 minutes per sample. RESULTS: Twenty clinicians recruited 93 patients (estimated 1:3 of all RTI cases). Patient's median age was 29, 57% female, and 44% with co-morbidities. Pre-test diagnoses: upper RTI (48%); lower RTI (30%); viral/influenza-like illness (18%); other (4%). Median set-up time was 2.72 minutes, with 72% swabs processed <4 hours, 90% <24 hours. Tests detected ≥1 virus in 58%, no pathogen 37% and atypical bacteria 2% (3% inconclusive). Antibiotics were prescribed pre-test to 35% of patients with no pathogen detected and 25% with a virus. Post-test diagnoses changed in 20%, and diagnostic certainty increased (P = 0.02), more so when the test was positive rather than negative (P < 0.001). Clinicians predicted decreased antibiotic benefit post-test (P = 0.02). Interviews revealed the POCT has clear potential, was easy to use and well-liked, but limited by time-to-result and the absence of testing for typical respiratory bacteria. CONCLUSIONS: This POCT was acceptable and appeared to influence clinical reasoning. Clinicians wanted faster time-to-results and more information about bacteria. Randomized trials are needed to understand the safety, efficacy and patient perceptions of these POCTs.


The UK government has called for the introduction of rapid diagnostics to curb overuse of antibiotics for common infections. Multi-viral respiratory 'point-of-care' tests (POCTs) are available but have not been used in UK primary care before. These POCTs use samples from the nose or back of the throat and give results quickly, to see if viruses or bacteria are there. In this study, four GP practices were given POCT machines for 6 weeks to see how they were used. Of the 93 patient samples tested, 3% were inconclusive, 37% tested negative, 58% had at least one virus and only 2% had a bacterial infection. Clinicians were more certain of patient diagnoses after testing especially when a virus or bacterium was detected and they were also less likely to predict the patient would benefit from antibiotics. Clinical diagnoses changed in 20% of patients after testing but less than 10% were contacted to change their treatment plan. During interviews, clinicians revealed they liked the test finding it easy-to-use but wanted faster time-to-results and testing for more bacteria. Clinical trials are needed to see if these POCTs can safely and cost-effectively reduce antibiotic prescribing in primary care.


Subject(s)
Respiratory Tract Infections , Viruses , Adult , Anti-Bacterial Agents/therapeutic use , Feasibility Studies , Female , Humans , Male , Point-of-Care Testing , Primary Health Care , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/drug therapy
7.
Infect Dis (Lond) ; 53(6): 420-429, 2021 06.
Article in English | MEDLINE | ID: covidwho-1096427

ABSTRACT

INTRODUCTION: A year into the pandemic, the knowledge of SARS-CoV-2 infection risks among healthcare workers remains limited. In this cross-sectional study, we examined whether healthcare workers with high exposure to Covid-19 patients had a higher risk of SARS-CoV-2 infection than other healthcare workers in a Norwegian University Hospital. We also investigated the prevalence of asymptomatic healthcare workers in a ward with a SARS-CoV-2 outbreak. METHODS: Healthcare workers from five wards at Akershus University Hospital were included between May 11 and June 11, 2020. Blood samples were analyzed for SARS-CoV-2 antibodies and seroprevalences compared between participants with high and low exposure to Covid-19 patients. Demographic data and SARS-CoV-2 infection risk factors were recorded in a questionnaire. Naso-/oropharyngeal swabs from participants from the outbreak ward were analyzed by reverse transcriptase-polymerase chain reaction. RESULTS: 360/436 (82.6%) healthcare workers participated. 9/262 (3.4%) participants from wards with high exposure to Covid-19 patients were SARS-CoV-2 seropositive versus 3/98 (3.1%) from wards with low exposure (OR 1.13; 95%CI 0.3-4.26, p = .861). SARS-CoV-2 antibodies were found in 11/263 (4.2%) participants who had worked one or more shifts caring for Covid-19 patients versus in 1/85 (1.2%) without any known occupational Covid-19 exposure (OR 3.67; 95%CI 0.46-29.06, p = .187). SARS-CoV-2 was detected in naso-/oropharyngeal swabs from 2/78 (2.6%) participants. CONCLUSION: We found no significantly increased risk of SARS-CoV-2 infection in healthcare workers with high exposure to COVID-19 patients. Five healthcare workers had either serologic or molecular evidence of past or present unrecognized SARS-CoV-2 infection.


Subject(s)
COVID-19 , SARS-CoV-2 , Cross-Sectional Studies , Health Personnel , Humans , Pandemics
8.
J Paediatr Child Health ; 57(7): 1078-1081, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1091030

ABSTRACT

AIM: The diagnosis of coronavirus disease 2019 (COVID-19) depends on accurate and rapid testing. Choosing an appropriate sample may impact diagnosis. Naso-oropharyngeal swabs (NOS) are most frequently used, despite several limitations. Since studies suggest nasopharyngeal aspirate (NPA) as a superior alternative in children, we hypothesised collecting both nasopharyngeal swab and aspirate would improve our diagnostic accuracy. METHODS: Observational, longitudinal, prospective study from 7 March to 7 May in a tertiary paediatric hospital in Lisbon. The objective was to compare the rate of detection of SARS-CoV-2 between NOS and NPA samples collected simultaneously. RESULTS: A total of 438 samples collected from 85 patients with confirmed COVID-19. There were 47.7% overall positive specimens - 32% (70/219) positive NOS and 63.5% (139/219) positive NPA. The tests were 67.6% concordant (k = 0.45). 50.3% had positive NPA with negative NOS, while 1.3% had positive NOS with negative NPA. NPA proved to be more sensitive (98.6% with 95% confidence interval 91.2-99.9% vs. 49.6% with 95% confidence interval 41.1-58.2%, P < 0.001). Additionally, the difference between NPA and NOS positive samples was statistically significant across all population groups (age, health condition, clinical presentation, contact with COVID-19 patients or need for hospitalisation), meaning NPA is more sensitive overall. CONCLUSIONS: Nasopharyngeal aspirates had greater sensitivity than naso-oropharyngeal swabs in detecting SARS-CoV-2. Our results suggest paediatric patients would benefit from collecting nasopharyngeal aspirates in hospital settings, whenever feasible, to improve diagnosis of COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Child , Humans , Nasopharynx , Prospective Studies , Specimen Handling
9.
Epidemiol Prev ; 44(5-6 Suppl 2): 128-135, 2020.
Article in Italian | MEDLINE | ID: covidwho-1068132

ABSTRACT

OBJECTIVES: to investigate the role of gender, age, province of residence, and nursing home residency on the risk of death for residents in the Friuli Venezia Giulia (FVG) Region (Northern Italy) tested positive for Covid-19, considering recovery as a competing event. The secondary objective is to describe the impact of the Covid-19 epidemic in FVG and in the Regions of Northern and Central Italy in terms of incidence and mortality compared to the national data. DESIGN: retrospective cohort study. SETTING AND PARTICIPANTS: resident population in FVG in the period between 29 February and 25 June 2020. MAIN OUTCOME MEASURES: in order to describe the impact of the Covid-19 outbreak in FVG, in terms of incidence and mortality compared to the national data, the standardized incidence (SIR) and mortality (SMR) ratios and their respective 95% confidence intervals (95%CI) were calculated compared to the Italian population for the northern and central Regions of Italy and the autonomous Provinces (PA) of Trento and Bolzano. A retrospective cohort study was conducted on subjects residing in FVG to whom at least one naso-oropharyngeal swab (hereafter, named swab) resulted positive for Covid-19. For each subject included in the cohort, the observation period started with the first positive swab and ended with the first of the following events: death, recovery or censored, which means that at the end of the observation period the subject was still alive and positive. The cause of death was assigned to Covid-19 if a subject had not yet recovered at the time when the event occurred. Cohort members were considered recovered after two negative consecutive swabs. The sub-hazard ratio (SHR) was estimated by applying the regression model of competing risks by Fine and Gray, in which the event of interest was the death caused by Covid-19 and the competing event was recovery. The explanatory variables included in the multiple models are: gender, age at the beginning of the observation period, the Province of residence, and nursing home residency. The cause-specific hazard was estimated using Cox proportional hazard regression. RESULTS: during the observation period, 3,305 cases and 345 deaths were recorded in FVG; SIR and SMR resulted, respectively, equal to 0.64 (95%CI 0.61-0.68) and 0.43 (95%CI 0.37-0.50). The FVG was the Northern Region one with the lowest incidence and mortality. The cohort consisted of 3,121 residents in FVG with at least one swab with a positive Covid-19 result during the study period. The SHR of dying for Covid-19 is equal to 16.13 (95%CI 9.73-26.74) for people with age 70-79 years and 35.58 (95%CI 21.77-58.15) with age >=80 years respect those with age <70 years. It is higher in males (SHR 1.71; 95%CI 1.34-2.17). There is no evidence that being resident in a nursing home affects the SHR (SHR 0.91 and 95%CI 0.69-1.20). As regards the province as an explanatory variable, the sub-hazard of death in the province of Trieste appears to overlap to the sub-hazard of Pordenone used as a reference; for the provinces of Udine and Gorizia the sub-hazards seem lower than the reference. CONCLUSIONS: while other Northern Regions and autonomous Provinces show higher standardized incidence and mortality compared with Italy, FVG and Veneto do not. In FVG, male gender and age are important determinants of death while there is no evidence that the condition of guest in a nursing home increases the sub-hazard of death.


Subject(s)
COVID-19/mortality , Pandemics , SARS-CoV-2 , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , Child , Child, Preschool , Female , Geography, Medical , Humans , Incidence , Infant , Infant, Newborn , Italy/epidemiology , Male , Middle Aged , Nursing Homes/statistics & numerical data , Proportional Hazards Models , Residence Characteristics , Retrospective Studies , Risk Assessment/statistics & numerical data , Risk Factors , Sex Factors , Young Adult
10.
PeerJ ; 9: e10599, 2021.
Article in English | MEDLINE | ID: covidwho-1043196

ABSTRACT

BACKGROUND: Cancer patients, especially those receiving cytotoxic therapy, are assumed to have a higher probability of death from COVID-19. We have conducted this study to identify the Case Fatality Rate (CFR) in cancer patients with COVID-19 and have explored the relationship of various clinical factors to mortality in our patient cohort. METHODS: All confirmed cancer cases presented to the hospital from June 8 to August 20, 2020, and developed symptoms/radiological features suspicious of COVID-19 were tested by Real-time polymerase chain reaction assay and/or cartridge-based nucleic acid amplification test from a combination of naso-oropharyngeal swab for SARS-CoV-2. Clinical data, treatment details, and outcomes were assessed from the medical records. RESULTS: Of the total 3,101 cancer patients admitted to the hospital, 1,088 patients were tested and 186 patients were positive for SARS-CoV-2. The CFR in the cohort was 27/186 (14.52%). Univariate analysis showed that the risk of death was significantly associated with the presence of any comorbidity (OR: 2.68; (95% CI [1.13-6.32]); P = 0.025), multiple comorbidities (OR: 3.01; (95% CI [1.02-9.07]); P = 0.047 for multiple vs. single), and the severity of COVID-19 presentation (OR: 27.48; (95% CI [5.34-141.49]); P < 0.001 for severe vs. not severe symptoms). Among all comorbidities, diabetes (OR: 3.31; (95% CI [1.35-8.09]); P = 0.009) and cardiovascular diseases (OR: 3.77; (95% CI [1.02-13.91]); P = 0.046) were significant risk factors for death. Anticancer treatments including chemotherapy, surgery, radiotherapy, targeted therapy, and immunotherapy administered within a month before the onset of COVID-19 symptoms had no significant effect on mortality. CONCLUSION: To the best of our knowledge, this is the first study from India reporting the CFR, clinical associations, and risk factors for mortality in SARS-CoV-2 infected cancer patients. Our study shows that the frequency of COVID-19 in cancer patients is high. Recent anticancer therapies are not associated with mortality. Pre-existing comorbidities, especially diabetes, multiple comorbidities, and severe symptoms at presentation are significantly linked with COVID-19 related death in the cohort.

11.
BMC Microbiol ; 21(1): 31, 2021 01 22.
Article in English | MEDLINE | ID: covidwho-1041745

ABSTRACT

BACKGROUND: Early 2020, a COVID-19 epidemic became a public health emergency of international concern. To address this pandemic broad testing with an easy, comfortable and reliable testing method is of utmost concern. Nasopharyngeal (NP) swab sampling is the reference method though hampered by international supply shortages. A new oropharyngeal/nasal (OP/N) sampling method was investigated using the more readily available throat swab. RESULTS: 35 patients were diagnosed with SARS-CoV-2 by means of either NP or OP/N sampling. The paired swabs were both positive in 31 patients. The one patient who tested negative on both NP and OP/N swab on admission, was ultimately diagnosed on bronchoalveolar lavage fluid. A strong correlation was found between the viral RNA loads of the paired swabs (r = 0.76; P < 0.05). The sensitivity of NP and OP/N analysis in hospitalized patients (n = 28) was 89.3% and 92.7% respectively. CONCLUSIONS: This study demonstrates equivalence of NP and OP/N sampling for detection of SARS-CoV-2 by means of rRT-PCR. Sensitivity of both NP and OP/N sampling is very high in hospitalized patients.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Pandemics , SARS-CoV-2/isolation & purification , Specimen Handling/methods , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Prospective Studies , Sensitivity and Specificity , Young Adult
12.
J Clin Microbiol ; 59(1)2020 12 17.
Article in English | MEDLINE | ID: covidwho-991745

ABSTRACT

Nucleic acid amplification for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory samples is the standard method for diagnosis. The majority of this testing is centralized and therefore has turnaround times of several days. Point-of-care (POC) testing with rapid turnaround times would allow more effective triage in settings where patient management and infection control decisions need to be made rapidly. The inclusivity and specificity of the Simple AMplification-Based Assay (SAMBA) II SARS-CoV-2 test were determined by both in silico analyses of the primers and probes and wet testing. The SAMBA II SARS-CoV-2 test was evaluated for performance characteristics. Clinical performance was evaluated in residual combined throat/nose swabs and compared to that of the Public Health England real-time PCR assay targeting the RdRp gene. The SAMBA II SARS-CoV-2 test has an analytical sensitivity of 250 copies/ml for detecting two regions of the genome (open reading frame 1ab [ORF1ab] and nucleocapsid protein [N]). The clinical performance was evaluated in 172 residual combined nose/throat swabs provided by the Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge (CMPHL), which showed an estimated positive percent agreement of 98.9% (95% confidence interval [CI], 93.83 to 99.97) and negative percent agreement of 96.4% (95% CI, 89.92 to 99.26) compared to testing by the CMPHL. The data show that the SAMBA II SARS-CoV-2 test performs equivalently to the centralized testing methods, but with a shorter turnaround time of 86 to 101 min. Point-of-care tests such as SAMBA should enable rapid patient management and effective implementation of infection control measures.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/genetics , Nucleic Acid Amplification Techniques/methods , Viral Proteins/genetics , Humans , Molecular Diagnostic Techniques/methods , Point-of-Care Testing , Polyproteins/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
13.
Emerg Med J ; 38(2): 94-99, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-934106

ABSTRACT

BACKGROUND: A promising modality for diagnosing pulmonary manifestations of COVID-19 in the emergency department (ED) is point-of-care ultrasound (POCUS) of the lungs. The currently used PCR as well as chest X-ray and CT scanning have important disadvantages. The aim of this study is to evaluate the diagnostic accuracy of POCUS in patients with suspected pulmonary manifestations of COVID-19 in the ED. METHODS: This prospective diagnostic accuracy study was conducted at the ED of our non-academic level 1 trauma centre (Isala, Zwolle, the Netherlands). Patients were enrolled between 14 April and 22 April 2020. Patients (aged ≥16 years) with suspected COVID-19 presenting to the ED underwent POCUS. All patients received current standard of care, including PCR (naso-oropharyngeal swab). Outcome of POCUS was compared with PCR or CT scan outcome to determine diagnostic accuracy. Diagnostic accuracy measures were calculated using 2×2 contingency tables. RESULTS: 100 patients were eligible to participate in this study, data of 93 patients were analysed. 27 (29%) patients were found positive for COVID-19 by PCR or CT. POCUS had a sensitivity of 89% (95% CI 70% to 97%), specificity of 59% (95% CI 46% to 71%), negative predictive value of 93% (95% CI 79% to 98%) and positive predictive value of 47% (95% CI 33% to 61%). In a subgroup of patients without previous cardiopulmonary disease (n=37), POCUS had a sensitivity of 100% (95% CI 70% to 100%), specificity of 76% (95% CI 54% to 90%), negative predictive value of 100% (95% CI 79% to 100%) and positive predictive value of 67% (95% CI 41% to 86%). CONCLUSION: POCUS of the lungs could serve as a valuable, radiation-free tool for excluding pulmonary manifestations of COVID-19 in patients in the ED at the point of assessment, especially in patients without previous cardiopulmonary disease. TRIAL REGISTRATION: Dutch Trial Register, No: NTR8544.


Subject(s)
COVID-19/diagnostic imaging , Lung/diagnostic imaging , Point-of-Care Testing , Ultrasonography , Aged , Aged, 80 and over , Emergency Service, Hospital , Female , Humans , Male , Middle Aged , Netherlands , Predictive Value of Tests , Prospective Studies
14.
BMJ Open ; 10(11): e042946, 2020 11 06.
Article in English | MEDLINE | ID: covidwho-913770

ABSTRACT

OBJECTIVES: To identify the diagnostic accuracy of common imaging modalities, chest X-ray (CXR) and CT, for diagnosis of COVID-19 in the general emergency population in the UK and to find the association between imaging features and outcomes in these patients. DESIGN: Retrospective analysis of electronic patient records. SETTING: Tertiary academic health science centre and designated centre for high consequence infectious diseases in London, UK. PARTICIPANTS: 1198 patients who attended the emergency department with paired reverse transcriptase PCR (RT-PCR) swabs for SARS-CoV-2 and CXR between 16 March and 16 April 2020. MAIN OUTCOME MEASURES: Sensitivity and specificity of CXR and CT for diagnosis of COVID-19 using the British Society of Thoracic Imaging reporting templates. Reference standard was any RT-PCR positive naso-oropharyngeal swab within 30 days of attendance. ORs of CXR in association with vital signs, laboratory values and 30-day outcomes were calculated. RESULTS: Sensitivity and specificity of CXR for COVID-19 diagnosis were 0.56 (95% CI 0.51 to 0.60) and 0.60 (95% CI 0.54 to 0.65), respectively. For CT scans, these were 0.85 (95% CI 0.79 to 0.90) and 0.50 (95% CI 0.41 to 0.60), respectively. This gave a statistically significant mean increase in sensitivity with CT of 29% (95% CI 19% to 38%, p<0.0001) compared with CXR. Specificity was not significantly different between the two modalities.CXR findings were not statistically significantly or clinically meaningfully associated with vital signs, laboratory parameters or 30-day outcomes. CONCLUSIONS: CT has substantially improved diagnostic performance over CXR in COVID-19. CT should be strongly considered in the initial assessment for suspected COVID-19. This gives potential for increased sensitivity and considerably faster turnaround time, where capacity allows and balanced against excess radiation exposure risk.


Subject(s)
COVID-19/diagnosis , Emergency Service, Hospital , Lung/diagnostic imaging , Propensity Score , Radiography, Thoracic/methods , SARS-CoV-2 , Tomography, X-Ray Computed/methods , COVID-19/epidemiology , COVID-19 Testing/methods , Data Management , Female , Humans , Male , Middle Aged , Pandemics , Retrospective Studies
15.
Wellcome Open Res ; 5: 141, 2020.
Article in English | MEDLINE | ID: covidwho-895726

ABSTRACT

Background: COVID-19 is a respiratory disease caused by a novel coronavirus (SARS-CoV-2) and causes substantial morbidity and mortality. There is currently no vaccine to prevent COVID-19 or therapeutic agent to treat COVID-19. This clinical trial is designed to evaluate chloroquine as a potential therapeutic for the treatment of hospitalised people with COVID-19. We hypothesise that chloroquine slows viral replication in patients with COVID-19, attenuating the infection, and resulting in more rapid decline of viral load in throat/nose swabs. This viral attenuation should be associated with improved patient outcomes. Method: The study will start with a 10-patient prospective observational pilot study following the same entry and exclusion criteria as for the randomized trial and undergoing the same procedures. The main study is an open label, randomised, controlled trial with two parallel arms of standard of care (control arm) versus standard of care with 10 days of chloroquine (intervention arm) with a loading dose over the first 24 hours, followed by 300mg base orally once daily for nine days. The study will recruit patients in three sites in Ho Chi Minh City, Vietnam: the Hospital for Tropical Diseases, the Cu Chi Field Hospital, and the Can Gio COVID hospital. The primary endpoint is the time to viral clearance from throat/nose swab, defined as the time following randomization until the midpoint between the last positive and the first of the negative throat/nose swabs. Viral presence will be determined using RT-PCR to detect SARS-CoV-2 RNA. Discussion: The results of the study will add to the evidence-based guidelines for management of COVID-19. Given the enormous experience of its use in malaria chemoprophylaxis, excellent safety and tolerability profile, and its very low cost, if proved effective then chloroquine would be a readily deployable and affordable treatment for patients with COVID-19. Trial registration: Clinicaltrials.gov NCT04328493 31/03/2020.

16.
Trials ; 21(1): 881, 2020 Oct 26.
Article in English | MEDLINE | ID: covidwho-892371

ABSTRACT

OBJECTIVES: The BCG vaccine, widely used in Brazil in new-borns, induces adjuvant protection for several diseases, including childhood virus infections. BCG activates monocytes and innate memory NK cells which are crucial for the antiviral immune response. Therefore, strategies to prevent COVID-19 in health workers (HW) should be carried out to prevent them becoming unwell so that they can continue to work during the pandemic. The hypothesis is that BCG will improve the innate immune response and prevent symptomatic infection or COVID-19 severity. The primary objective is to verify the effectiveness and safety of the BCG vaccine to prevent or reduce incidence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in the city of Goiânia (Brazil) among HW previously vaccinated with BCG and also its severity and mortality during the pandemic of the disease. Secondary objectives are to estimate the incidence of COVID-19 among these professionals and the innate immune response elicited to BCG. TRIAL DESIGN: This a phase II trial for repositioning BCG as a preventive strategy against COVID-19. The trial is an open-label, parallel-group randomised clinical trial, comparing HW vaccinated with BCG and HW not vaccinated. PARTICIPANTS: The trial will recruit 800 HW of Goiânia - Goiás, Brazil to reach a total of 400 HW included after comorbidities questioning and laboratorial evaluation. Eligibility criteria: Any HW presenting BCG vaccination scar with direct contact with suspected COVID-19 patients for at least 8 hours per week, whether in hospital beds, ICU, or in transportation or admission (nurses, doctors, physiotherapists, nutritionists, receptionists, etc.) who have negative IgM and IgG COVID-19 test. Participants with any of the following characteristics will be excluded: - Have had in the last fifteen days any signs or symptoms of virus infection, including COVID-19; - Have had fever in the last fifteen days; - Have been vaccinated fifteen days before the inclusion; - Have a history or confirmation of any immunosuppressive disease such as HIV, presented solid tumour in the last two years or autoimmune diseases; - Are under preventive medication with antibiotics, steroid anti-inflammatories, or chemotherapy; - Have less than 500 neutrophils per mL of blood; - Have previously been diagnosed with tuberculosis; - Are breastfeeding or pregnant; - Are younger than 18 years old; - Are participating as an investigator in this clinical trial. INTERVENTION AND COMPARATOR: HW will be randomized into the BCG vaccinated group or the BCG unvaccinated control group. The BCG vaccinated group will receive in the right arm, intradermally, a one off dose of 0.1 mL corresponding to approximately 2 x105 to 8 x105 CFU of live, freeze-dried, attenuated BCG Moscow 361-I, Bacillus Calmette Guerin vaccine (Serum Institute of India PVT. LTD.). The unvaccinated control group will not be vaccinated. The HW allocated in both groups will be followed up at specific times points until 180 days post inclusion. The vaccinated and control groups will be compared according to COVID-19 related outcomes. MAIN OUTCOMES: The primary outcomes are the incidence coefficient of infection by SARS-CoV-2 determined by RT-PCR of naso-oropharyngeal swab specimen or rapid lateral flow IgG and IgM test, and presence of general COVID-19 symptoms, disease severity and admission to hospital during the 180 days of follow up. The secondary outcome is the innate immune response elicited 15-20 days after vaccination. RANDOMISATION: The vaccine vial contains approximately 10 doses. In order to optimize the vaccine use, the randomisation was performed in blocks of 20 participants using the platform randomization.com [ http://www.jerrydallal.com/random/permute.htm ]. The randomization was prepared before any HW inclusion. The results were printed and inserted in sealed envelopes that were numbered with BCG-001 to BCG-400. The printed results as well the envelopes had the same numbers. At the time of the randomisation, each participant that meets the inclusion criteria will receive a consecutive participant number [BCG-001-BCG-400]. The sealed envelope with the assigned number, blinded to the researchers, will be opened in front of the participant and the arm allocation will be known. BLINDING (MASKING): There is no masking for the participants or for the healthcare providers. The study will be blinded to the laboratory researchers and to those who will be evaluating the outcomes and performing the statistical analyses. In this case, only the participant identification number will be available. NUMBERS TO BE RANDOMISED (SAMPLE SIZE): Four hundred heath workers will be randomised in two groups. Two hundred participants will be vaccinated, and 200 participants will not be vaccinated. TRIAL STATUS: The protocol approved by the Brazilian Ethical Committee is the seventh version, number CAAE: 31783720.0.0000.5078. The trial has been recruiting since September 20th, 2020. The clinical trial protocol was registered on August 5th, 2020. It is estimated that recruitment will finish by March 2021. TRIAL REGISTRATION: The protocol number was registered on August 5th, 2020 at REBEC (Registro Brasileiro de Ensaios Clínicos). Register number: RBR-4kjqtg and WHO trial registration number UTN: U1111-1256-3892. FULL PROTOCOL: The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1). In the interest in expediting dissemination of this material, the familiar formatting has been eliminated; this Letter serves as a summary of the key elements of the full protocol.


Subject(s)
BCG Vaccine/administration & dosage , Coronavirus Infections/prevention & control , Immunity, Innate/immunology , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Betacoronavirus/immunology , Brazil/epidemiology , COVID-19 , Case-Control Studies , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Cross Protection/immunology , Follow-Up Studies , Health Personnel/statistics & numerical data , Hospitalization/statistics & numerical data , Humans , Immunization, Secondary/methods , Immunoglobulin G/blood , Immunoglobulin M/blood , Incidence , Injections, Intradermal , Killer Cells, Natural/immunology , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2 , Safety , Treatment Outcome
17.
Front Med (Lausanne) ; 7: 576162, 2020.
Article in English | MEDLINE | ID: covidwho-874499

ABSTRACT

Objectives: To describe our experience with a coronavirus disease 2019 (COVID-19) outbreak within a large rheumatology department early in the pandemic. Methods: Symptomatic and asymptomatic healthcare workers (HCWs) had a naso-oropharyngeal swab for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and were followed clinically. Reverse transcription polymerase-chain reaction (RT-PCR) was repeated to document cure, and serological response was assessed. Patients with risk contacts within the department in the 14 days preceding the outbreak were screened for COVID-19 symptoms. Results: 14/34 HCWs (41%; 40 ± 14 years, 71% female) tested positive for SARS-CoV-2, and 11/34 (32%) developed symptoms but were RT-PCR-negative. Half of RT-PCR-positive HCWs did not report fever, cough, or dyspnea before testing, which were absent in 3/14 cases (21%). Mild disease prevailed (79%), but 3 HCWs had moderate disease requiring further assessment, which excluded severe complications. Nevertheless, symptom duration (28 ± 18 days), viral shedding (31 ± 10 days post-symptom onset, range 15-51), and work absence (29 ± 28 days) were prolonged. 13/14 (93%) of RT-PCR-positive and none of the RT-PCR-negative HCWs had a positive humoral response Higher IgG indexes were observed in individuals over 50 years of age (14.5 ± 7.7 vs. 5.0 ± 4.4, p = 0.012). Of 617 rheumatic patients, 8 (1.3%) developed COVID-19 symptoms (1/8 hospitalization, 8/8 complete recovery), following a consultation/procedure with an asymptomatic (7/8) or mildly symptomatic (1/8) HCW. Conclusions: A COVID-19 outbreak can occur among HCWs and rheumatic patients, swiftly spreading over the presymptomatic stage. Mild disease without typical symptoms should be recognized and may evolve with delayed viral shedding, prolonged recovery, and adequate immune response in most individuals.

18.
Gene Rep ; 21: 100910, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-837457

ABSTRACT

We decided to examine suspected samples of pneumonia outbreak caused by the new coronavirus SARS-CoV-2 and provide information about the mortality rate due to this infection in different age groups in Iran. In this descriptive-cross-sectional study, a total of 784 samples of naso/oropharyngeal swabs of suspected patients with COVID-19 symptoms who had referred to Imam Khomeini, Shahid Fayaz-Bakhsh and Modarres hospitals in Tehran from February 24, 2020 to March 24, 2020 were examined by RT-PCR method. The highest incidence of the disease was within the age group of 50-59 years, while the lowest rate was in the 0-9 years age group. The highest rate of positive samples in terms of COVID-19 among suspected individuals was for patients >80 years of age (89%) and the highest mortality rate was in the age range of 70-79 years (31%) and >80 years (30), respectively. In terms of recovery, the highest rate was in the 30-39 years age group (65.2%). Statistical analysis showed that mortality significantly increased in the age group of >60 years old and in fact, mortality was significantly associated with older ages. According to the results of the current study, the prevalence of COVID-19 in lower age (0-9 years old) is lower and mortality rate is higher in older ages as significant increase in mortality was observed in those aged >60 years old. However, further epidemiological studies on a larger study population in different regions of Iran are needed to explain the prevalence, clinical features, and course of the disease.

19.
bioRxiv ; 2020 May 01.
Article in English | MEDLINE | ID: covidwho-823190

ABSTRACT

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.

20.
J Infect Dis ; 222(8): 1270-1279, 2020 09 14.
Article in English | MEDLINE | ID: covidwho-811304

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)-recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs. METHODS: Nasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2. RESULTS: The Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%). CONCLUSIONS: Winter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.


Subject(s)
Coinfection/epidemiology , Communicable Diseases, Emerging/epidemiology , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Respiratory Tract Infections/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Child , Child, Preschool , Clinical Laboratory Techniques , Coinfection/immunology , Coinfection/virology , Communicable Diseases, Emerging/virology , Coronavirus Envelope Proteins , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Coronavirus Nucleocapsid Proteins , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Nucleocapsid Proteins/genetics , Pandemics , Phosphoproteins , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Respiratory Tract Infections/virology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics , Viral Envelope Proteins , World Health Organization , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL