Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 57
Filter
1.
Cell Host Microbe ; 27(6): 879-882.e2, 2020 06 10.
Article in English | MEDLINE | ID: covidwho-1719463

ABSTRACT

The inflammatory response to SARS-coronavirus-2 (SARS-CoV-2) infection is thought to underpin COVID-19 pathogenesis. We conducted daily transcriptomic profiling of three COVID-19 cases and found that the early immune response in COVID-19 patients is highly dynamic. Patient throat swabs were tested daily for SARS-CoV-2, with the virus persisting for 3 to 4 weeks in all three patients. Cytokine analyses of whole blood revealed increased cytokine expression in the single most severe case. However, most inflammatory gene expression peaked after respiratory function nadir, except expression in the IL1 pathway. Parallel analyses of CD4 and CD8 expression suggested that the pro-inflammatory response may be intertwined with T cell activation that could exacerbate disease or prolong the infection. Collectively, these findings hint at the possibility that IL1 and related pro-inflammatory pathways may be prognostic and serve as therapeutic targets for COVID-19. This work may also guide future studies to illuminate COVID-19 pathogenesis and develop host-directed therapies.


Subject(s)
Coronavirus Infections/genetics , Coronavirus Infections/immunology , Pneumonia, Viral/genetics , Pneumonia, Viral/immunology , Adult , Aged , Biological Variation, Individual , COVID-19 , Cluster Analysis , Coronavirus Infections/blood , Coronavirus Infections/pathology , Cytokines/blood , Gene Expression Regulation , Humans , Male , Pandemics , Pneumonia, Viral/blood , Pneumonia, Viral/pathology , Transcriptome , Up-Regulation
2.
Prenat Diagn ; 41(8): 998-1008, 2021 07.
Article in English | MEDLINE | ID: covidwho-1544370

ABSTRACT

OBJECTIVE: Identify the potential for and risk factors of SARS-CoV-2 vertical transmission. METHODS: Symptomatic pregnant women with COVID-19 diagnosis in whom PCR for SARS-CoV-2 was performed at delivery using maternal serum and at least one of the biological samples: cord blood (CB), amniotic fluid (AF), colostrum and/or oropharyngeal swab (OPS) of the neonate. The association of parameters with maternal, AF and/or CB positivity and the influence of SARS-CoV-2 positivity in AF and/or CB on neonatal outcomes were investigated. RESULTS: Overall 73.4% (80/109) were admitted in hospital due to COVID-19, 22.9% needed intensive care and there were four maternal deaths. Positive RT-PCR for SARS-CoV-2 was observed in 14.7% of maternal blood, 13.9% of AF, 6.7% of CB, 2.1% of colostrum and 3.7% of OPS samples. The interval between COVID-19 symptoms and delivery was inversely associated with SARS-CoV-2 positivity in the maternal blood (p = 0.002) and in the AF and/or CB (p = 0.049). Maternal viremia was associated with positivity for SARS-CoV-2 in AF and/or CB (p = 0.001). SARS-CoV-2 positivity in the compartments was not associated with neonatal outcomes. CONCLUSION: Vertical transmission is possible in pregnant women with COVID-19 and a shorter interval between maternal symptoms and delivery is an influencing factor.


Subject(s)
COVID-19/transmission , Infectious Disease Transmission, Vertical/statistics & numerical data , Pregnancy Complications, Infectious/virology , SARS-CoV-2/isolation & purification , Adult , Amniotic Fluid/virology , Brazil/epidemiology , COVID-19/mortality , COVID-19/virology , Colostrum/virology , Female , Humans , Infant, Newborn , Male , Pregnancy , Pregnancy Complications, Infectious/mortality , Prospective Studies , Young Adult
3.
Proteomics ; 21(7-8): e2000226, 2021 04.
Article in English | MEDLINE | ID: covidwho-1384280

ABSTRACT

A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here, we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Viral peptides were chosen as an example, because virology is an area where in silico library generation could significantly improve PRM assay design. With both libraries a total of 1174 precursors were identified. Notably, compared to the DDA-derived library, we could identify 101 more precursors by using the Prosit-derived library. Additionally, we show that Prosit can be applied to predict tandem mass spectra of synthetic viral peptides with different collision energies. Finally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab demonstrating that both libraries are suited for peptide identification by PRM. Summarized, Prosit-derived viral spectral libraries predicted in silico can be used for PRM data analysis, making DDA analysis for library generation partially redundant in the future.


Subject(s)
COVID-19/virology , Proteomics/methods , SARS-CoV-2/chemistry , Viral Proteins/analysis , Amino Acid Sequence , Humans , Neural Networks, Computer , Peptide Library , Peptides/analysis , Tandem Mass Spectrometry/methods
4.
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
5.
PLoS One ; 16(6): e0252611, 2021.
Article in English | MEDLINE | ID: covidwho-1264216

ABSTRACT

The present global pandemic triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has lingered for over a year in its devastating effects. Diagnosis of coronavirus disease 2019 (COVID-19) is currently established with a polymerase chain reaction (PCR) test by means of oropharyngeal-, nasopharyngeal-, anal-swabs, sputum and blood plasma. However, oral and nasal swabs are more commonly used. This study, therefore, assessed sensitivity and specificity of plasma as a diagnostic in comparison with a combination of oral and nasal swab samples, and the implications for blood transfusion. Oropharyngeal (OP) and nasopharyngeal (NP) swab samples were obtained from 125 individuals suspected to have COVID-19 and stored in viral transport medium (VTM) tubes. Ten millilitres of blood samples in EDTA were also obtained by venepuncture and spun to obtain plasma. Viral RNA was obtained from both swabs and plasma by manual extraction with Qiagen QIAamp viral RNA Mini Kit. Detection was done using a real time fluorescent RT-qPCR BGI kit, on a QuantStudio 3 real-time PCR instrument. Average age of study participants was 41 years, with 74 (59.2%) being male. Out of the 125 individuals tested for COVID-19, 75 (60%) were positive by OP/NP swab. However, only 6 (4.8%) had a positive plasma result for COVID-19 with median Ct value of 32.4. Sensitivity and specificity of RT-PCR SARS-CoV-2 test using plasma was 8% and 100% respectively. There was no false positive recorded, but 69 (55.2%) false negatives were obtained by plasma. SARS-CoV-2 viral RNA was detected, albeit low (4.8%) in plasma. Plasma is likely not a suitable biological sample to diagnose acute SARS-CoV-2 infection. The implication of transfusing blood in this era of COVID-19 needs further investigations.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , RNA, Viral/analysis , SARS-CoV-2/isolation & purification , Adolescent , Adult , Aged , COVID-19/blood , COVID-19/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Nigeria/epidemiology , RNA, Viral/blood , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Young Adult
6.
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
7.
BMJ Open ; 11(6): e051415, 2021 06 08.
Article in English | MEDLINE | ID: covidwho-1262401

ABSTRACT

OBJECTIVE: This study investigated seroprevalence of SARS-CoV-2-specific IgG antibodies, using the Abbott antinucleocapsid IgG chemiluminescent microparticle immunoassay (CMIA) assay, in five prespecified healthcare worker (HCW) subgroups following the first wave of the COVID-19 pandemic. SETTING: An 800-bed tertiary-level teaching hospital in the south of Ireland. PARTICIPANTS: Serum was collected for anti-SARS-CoV-2 nucleocapsid IgG using the Abbott ARCHITECT SARS-CoV-2 IgG CMIA qualitative assay, as per the manufacturer's specifications.The groups were as follows: (1) HCWs who had real-time PCR (RT-PCR) confirmed COVID-19 infection (>1-month postpositive RT-PCR); (2) HCWs identified as close contacts of persons with COVID-19 infection and who subsequently developed symptoms (virus not detected by RT-PCR on oropharyngeal/nasopharyngeal swab); (3) HCWs identified as close contacts of COVID-19 cases and who remained asymptomatic (not screened by RT-PCR); (4) HCWs not included in the aforementioned groups working in areas determined as high-risk clinical areas; and (5) HCWs not included in the aforementioned groups working in areas determined as low-risk clinical areas. RESULTS: Six of 404 (1.49%) HCWs not previously diagnosed with SARS-CoV-2 infection (groups 2-5) were seropositive for SARS-CoV-2 at the time of recruitment into the study.Out of the 99 participants in group 1, 72 had detectable IgG to SARS-CoV-2 on laboratory testing (73%). Antibody positivity correlated with shorter length of time between RT-PCR positivity and antibody testing.Quantification cycle value on RT-PCR was not found to be correlated with antibody positivity. CONCLUSIONS: Seroprevalence of SARS-CoV-2 antibodies in HCWs who had not previously tested RT-PCR positive for COVID-19 was low compared with similar studies.


Subject(s)
COVID-19 , Pandemics , Antibodies, Viral , Health Personnel , Humans , Ireland/epidemiology , SARS-CoV-2 , Seroepidemiologic Studies
8.
Microchem J ; 168: 106445, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1240512

ABSTRACT

Amid the global threat caused by the coronavirus disease 2019 (COVID-19) pandemic, developing sufficiently rapid, accurate, sensitive and selective methods of diagnosing both symptomatic and asymptomatic cases is essential to alleviating and controlling the pandemic's effects. This article describes an electrochemical immunoassay platform developed to determine the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) spike antibody by using gold-clusters capped with cysteamine, glutaraldehyde, the spike protein of the SARS-CoV-2 antigen and bovine serum albumin on a glassy carbon electrode. The electrochemical oxidation signal of the antigen-based immunosensor at 0.9 V was used to detect the SARS-CoV-2 spike antibody. When saliva and oropharyngeal swab samples were analysed, the recovery and relative standard deviation values were 96.97%-101.99% and 4.99%-5.74%, respectively. The method's limit of detection relative to the SARS-CoV-2 spike antibody in synthetic media and in saliva or oropharyngeal swab samples was 0.01 ag/mL, while the immunosensor's linear response to the SARS-CoV-2 spike antibody varied from 0.1 to 1000 ag/mL. The cross-reactivity of the Middle East respiratory syndrome-coronavirus spike antigen was evaluated after being immobilised onto the functionalised gold-cluster based sensor, indicated that the good specifity of the produced immunosensor.

9.
J Clin Med ; 10(10)2021 May 13.
Article in English | MEDLINE | ID: covidwho-1227038

ABSTRACT

Background Antigen-detecting rapid diagnostic tests (Ag-RDT) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) offer new opportunities for the quick and laboratory-independent identification of infected individuals for control of the SARS-CoV-2 pandemic. Despite the potential benefits, nasopharyngeal sample collection is frequently perceived as uncomfortable by patients and requires trained healthcare personnel with protective equipment. Therefore, anterior nasal self-sampling is increasingly recognized as a valuable alternative. Methods We performed a prospective, single-center, point of care validation of an Ag-RDT using a polypropylene absorbent collector for standardized self-collected anterior nasal swabs. Real-time polymerase chain reaction (RT-PCR) from combined oropharyngeal/nasopharyngeal swabs served as a comparator. Primary endpoint was sensitivity of the standardized Ag-RDT in symptomatic patients with medium or high viral concentration (≥1 million RNA copies on RT-PCR for SARS-CoV-2). Results Between 12 February and 22 March 2021, 388 participants were enrolled. After exclusion of 9 patients for which no PCR result could be obtained, the novel Ag-RDT was evaluated based on 379 participants, of whom 273 were symptomatic and 106 asymptomatic. In 61 samples from symptomatic patients with medium or high viral load (≥1 million RNA copies), the sensitivity of the standardized Ag-RDT was 96.7% (59/61; 95% confidence interval (CI): 88.7-99.6%) for the primary endpoint. In total, 62 positive Ag-RDT results were detected out of 70 RT-PCR positive individuals, yielding an overall sensitivity of 88.6% (95% CI: 78.7-94.9%). Specificity was 99.7% (95% CI: 98.2-100%) in 309 RT-PCR negative individuals. Conclusions Here, we present a validation of a novel Ag-RDT with a standardized sampling process for anterior nasal self-collection, which meets World Health Organisation (WHO) criteria of ≥80% sensitivity and ≥97% specificity. Although less sensitive than RT-PCR, this assay could be beneficial due to its rapid results, ease of use, and suitability for standardized self-testing.

10.
Virol Sin ; 36(5): 901-912, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1182321

ABSTRACT

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background. To address this issue, we modified and evaluated an approach by utilizing SARS-CoV-2-specific amplicon amplification and Oxford Nanopore PromethION platform. This workflow started with the throat swab of the COVID-19 patient, combined reverse transcript PCR, and multi-amplification in one-step to shorten the experiment time, then can quickly and steadily obtain high-quality SARS-CoV-2 genome within 24 h. A comprehensive evaluation of the method was conducted in 42 samples: the sequencing quality of the method was correlated well with the viral load of the samples; high-quality SARS-CoV-2 genome could be obtained stably in the samples with Ct value up to 39.14; data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20; variation analysis indicated that the method can detect the existing and emerging genomic mutations as well; Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing, making it as low as 0.4/10,000 bp. In summary, high-quality SARS-CoV-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARS-CoV-2.


Subject(s)
COVID-19 , Nanopore Sequencing , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Pandemics , RNA, Viral/genetics , SARS-CoV-2
11.
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
12.
PLoS One ; 16(3): e0248371, 2021.
Article in English | MEDLINE | ID: covidwho-1147457

ABSTRACT

Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.


Subject(s)
Genetic Variation , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Aged, 80 and over , COVID-19/pathology , COVID-19/virology , Female , Gene Deletion , Humans , Male , Middle Aged , Mutation, Missense , Oropharynx/virology , Pakistan , Phylogeny , RNA, Viral/chemistry , RNA, Viral/isolation & purification , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/metabolism , Whole Genome Sequencing , Young Adult
13.
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
14.
Int J Infect Dis ; 105: 709-715, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1135364

ABSTRACT

BACKGROUND: The spectrum of COVID-19 clinical manifestations is not yet known. In the elderly, mortality and extrapulmonary involvement appears more frequent than expected. METHODS: A multicentre-retrospective-case-series study of COVID-19 patients, aged ≥65 years, hospitalised between March 1 and June 15, 2020. Patients were classified at admission into 3 groups based on their Clinical Frailty Scale (CFS) score: 1-3 (group A), 4-6 (group B) and 7-9 (group C). RESULTS: Of the 206 patients in the study, 60 (29%) were assigned to group A, 60 (29%) to B and 86 (42%) to C. Significantly more frequent in group C than in B or A were: mental confusion (respectively 65%, 33%, 7%; P < 0.001), kidney failure (39%, 22%, 20%; P = 0.019), dehydration syndrome (55%, 27%, 13%; P < 0.001), electrolyte imbalance (54%, 32%, 25%; P = 0.001), and diabetic decompensation (22%, 12%, 7%; P = 0.026). Crude mortality was 27%. By multivariate logistic regression model independent predictors of death were male sex (adjusted odds ratio (aOR) = 2.87,95%CI = 1.15-7.18), CFS 7-9 (aOR = 9.97,95%CI = 1.82-52.99), dehydration at admission (aOR = 4.27,95%CI = 1.72-10.57) and non-invasive/invasive ventilation (aOR = 4.88,95%CI = 1.94-12.26). CONCLUSIONS: Elderly patients with a high CFS showed frequent extrapulmonary signs at admission, even in the absence of lung involvement. These findings, along with a high CFS, predicted a significant risk of mortality.


Subject(s)
COVID-19/diagnosis , COVID-19/mortality , Aged , Aged, 80 and over , COVID-19/complications , Cohort Studies , Female , Frailty , Hospitalization , Humans , Logistic Models , Male , Odds Ratio , Retrospective Studies , SARS-CoV-2
15.
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
16.
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
17.
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
18.
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
19.
Diagn Progn Res ; 5(1): 4, 2021 Feb 08.
Article in English | MEDLINE | ID: covidwho-1069608

ABSTRACT

BACKGROUND: The aim of RApid community Point-of-care Testing fOR COVID-19 (RAPTOR-C19) is to assess the diagnostic accuracy of multiple current and emerging point-of-care tests (POCTs) for active and past SARS-CoV2 infection in the community setting. RAPTOR-C19 will provide the community testbed to the COVID-19 National DiagnOstic Research and Evaluation Platform (CONDOR). METHODS: RAPTOR-C19 incorporates a series of prospective observational parallel diagnostic accuracy studies of SARS-CoV2 POCTs against laboratory and composite reference standards in patients with suspected current or past SARS-CoV2 infection attending community settings. Adults and children with suspected current SARS-CoV2 infection who are having an oropharyngeal/nasopharyngeal (OP/NP) swab for laboratory SARS-CoV2 reverse transcriptase Digital/Real-Time Polymerase Chain Reaction (d/rRT-PCR) as part of clinical care or community-based testing will be invited to participate. Adults (≥ 16 years) with suspected past symptomatic infection will also be recruited. Asymptomatic individuals will not be eligible. At the baseline visit, all participants will be asked to submit samples for at least one candidate point-of-care test (POCT) being evaluated (index test/s) as well as an OP/NP swab for laboratory SARS-CoV2 RT-PCR performed by Public Health England (PHE) (reference standard for current infection). Adults will also be asked for a blood sample for laboratory SARS-CoV-2 antibody testing by PHE (reference standard for past infection), where feasible adults will be invited to attend a second visit at 28 days for repeat antibody testing. Additional study data (e.g. demographics, symptoms, observations, household contacts) will be captured electronically. Sensitivity, specificity, positive, and negative predictive values for each POCT will be calculated with exact 95% confidence intervals when compared to the reference standard. POCTs will also be compared to composite reference standards constructed using paired antibody test results, patient reported outcomes, linked electronic health records for outcomes related to COVID-19 such as hospitalisation or death, and other test results. DISCUSSION: High-performing POCTs for community use could be transformational. Real-time results could lead to personal and public health impacts such as reducing onward household transmission of SARS-CoV2 infection, improving surveillance of health and social care staff, contributing to accurate prevalence estimates, and understanding of SARS-CoV2 transmission dynamics in the population. In contrast, poorly performing POCTs could have negative effects, so it is necessary to undertake community-based diagnostic accuracy evaluations before rolling these out. TRIAL REGISTRATION: ISRCTN, ISRCTN14226970.

20.
Indian J Pediatr ; 88(8): 800-801, 2021 08.
Article in English | MEDLINE | ID: covidwho-1068809

ABSTRACT

There are concerns regarding the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from mother to child during this COVID pandemic. This descriptive study was done to check the possible transmission of the virus through breastfeeding in the Indian context. RT-qPCR for SARS-CoV-2 was done in breast milk samples from 30 COVID-positive mothers. Paired oropharyngeal swabs of the same neonates were also sent for RT-PCR at 48 h and on day 5 of life. All the breast milk samples were negative for SARS-CoV-2 except one. A repeat sample of breast milk from the same mother was also negative when rechecked the next day. All the paired neonatal oropharyngeal swabs were also negative for SARS-CoV-2. The authors could not find evidence for transmission of SARS-CoV-2 from mother to child through breastmilk in the population studied.


Subject(s)
COVID-19 , SARS-CoV-2 , Breast Feeding , Child , Female , Humans , Infant, Newborn , Infectious Disease Transmission, Vertical , Mothers
SELECTION OF CITATIONS
SEARCH DETAIL