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1.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327526

ABSTRACT

ABSTRACT The ability to distinguish between SARS-CoV-2 variants of concern (VOCs) is of ongoing interest due to differences in transmissibility, response to vaccination, clinical prognosis, and therapy. Although detailed genetic characterization requires whole-genome sequencing (WGS), targeted nucleic acid amplification tests can serve a complementary role in clinical settings, as they are more rapid and accessible than sequencing in most laboratories. We designed and analytically validated a two-reaction multiplex reverse transcription quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in Reaction 1, and del69-70, K417N, and T478K in Reaction 2. This assay had 95-100% agreement with WGS in 502 upper respiratory swabs collected between April 26 and August 1, 2021, consisting of 43 Alpha, 2 Beta, 20 Gamma, 378 Delta, and 59 non-VOC infections. Validation in a separate group of 230 WGS-confirmed Omicron variant samples collected in December 2021 and January 2022 demonstrated 100% agreement. This RT-qPCR-based approach can be implemented in clinical laboratories already performing SARS-CoV-2 nucleic acid amplification tests to assist in local epidemiological surveillance and clinical decision-making.

3.
J Clin Microbiol ; 59(8): e0085921, 2021 Jul 19.
Article in English | MEDLINE | ID: covidwho-1494947

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase PCR (RT-qPCR) to detect three nonsynonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2-positive specimens from our San Francisco Bay Area population. Between 1 December 2020 and 1 March 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K plus N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing of a validation subset of 229 specimens and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed the rapid emergence of the L452R variant in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.


Subject(s)
COVID-19 , SARS-CoV-2 , Epidemiological Monitoring , Genotype , Humans , Reverse Transcriptase Polymerase Chain Reaction
4.
Emerg Infect Dis ; 27(10): 2720-2723, 2021.
Article in English | MEDLINE | ID: covidwho-1486743

ABSTRACT

We report persistent severe acute respiratory syndrome coronavirus 2 infection in a patient with HIV/AIDS; the virus developed spike N terminal domain and receptor binding domain neutralization resistance mutations. Our findings suggest that immunocompromised patients can harbor emerging variants of severe acute respiratory syndrome coronavirus 2.


Subject(s)
Acquired Immunodeficiency Syndrome , COVID-19 , Humans , Mutation , Protein Binding , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
5.
Clin Chem ; 68(1): 204-213, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-1450383

ABSTRACT

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen in blood has been described, but the diagnostic and prognostic role of antigenemia is not well understood. This study aimed to determine the frequency, duration, and concentration of nucleocapsid antigen in plasma and its association with coronavirus disease 2019 (COVID-19) severity. METHODS: We utilized an ultrasensitive electrochemiluminescence immunoassay targeting SARS-CoV-2 nucleocapsid antigen to evaluate 777 plasma samples from 104 individuals with COVID-19. We compared plasma antigen to respiratory nucleic acid amplification testing (NAAT) in 74 individuals with COVID-19 from samples collected ±1 day of diagnostic respiratory NAAT and in 52 SARS-CoV-2-negative individuals. We used Kruskal-Wallis tests, multivariable logistic regression, and mixed-effects modeling to evaluate whether plasma antigen concentration was associated with disease severity. RESULTS: Plasma antigen had 91.9% (95% CI 83.2%-97.0%) clinical sensitivity and 94.2% (84.1%-98.8%) clinical specificity. Antigen-negative plasma samples belonged to patients with later respiratory cycle thresholds (Ct) when compared with antigen-positive plasma samples. Median plasma antigen concentration (log10 fg/mL) was 5.4 (interquartile range 3.9-6.0) in outpatients, 6.0 (5.4-6.5) in inpatients, and 6.6 (6.1-7.2) in intensive care unit (ICU) patients. In models adjusted for age, sex, diabetes, and hypertension, plasma antigen concentration at diagnosis was associated with ICU admission [odds ratio 2.8 (95% CI 1.2-6.2), P=.01] but not with non-ICU hospitalization. Rate of antigen decrease was not associated with disease severity. CONCLUSIONS: SARS-CoV-2 plasma nucleocapsid antigen exhibited comparable diagnostic performance to upper respiratory NAAT, especially among those with late respiratory Ct. In addition to currently available tools, antigenemia may facilitate patient triage to optimize intensive care utilization.


Subject(s)
Antigens, Viral/blood , COVID-19 Testing/methods , COVID-19 , Coronavirus Nucleocapsid Proteins/blood , COVID-19/diagnosis , Electrochemical Techniques , Hospitalization , Humans , Immunoassay , Luminescent Measurements , Nucleocapsid , Phosphoproteins/blood , SARS-CoV-2 , Sensitivity and Specificity
6.
EBioMedicine ; 71: 103546, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1363149

ABSTRACT

BACKGROUND: Respiratory virus infections are significant causes of morbidity and mortality, and may induce host metabolite alterations by infecting respiratory epithelial cells. We investigated the use of liquid chromatography quadrupole time-of-flight mass spectrometry (LC/Q-TOF) combined with machine learning for the diagnosis of influenza infection. METHODS: We analyzed nasopharyngeal swab samples by LC/Q-TOF to identify distinct metabolic signatures for diagnosis of acute illness. Machine learning models were performed for classification, followed by Shapley additive explanation (SHAP) analysis to analyze feature importance and for biomarker discovery. FINDINGS: A total of 236 samples were tested in the discovery phase by LC/Q-TOF, including 118 positive samples (40 influenza A 2009 H1N1, 39 influenza H3 and 39 influenza B) as well as 118 age and sex-matched negative controls with acute respiratory illness. Analysis showed an area under the receiver operating characteristic curve (AUC) of 1.00 (95% confidence interval [95% CI] 0.99, 1.00), sensitivity of 1.00 (95% CI 0.86, 1.00) and specificity of 0.96 (95% CI 0.81, 0.99). The metabolite most strongly associated with differential classification was pyroglutamic acid. Independent validation of a biomarker signature based on the top 20 differentiating ion features was performed in a prospective cohort of 96 symptomatic individuals including 48 positive samples (24 influenza A 2009 H1N1, 5 influenza H3 and 19 influenza B) and 48 negative samples. Testing performed using a clinically-applicable targeted approach, liquid chromatography triple quadrupole mass spectrometry, showed an AUC of 1.00 (95% CI 0.998, 1.00), sensitivity of 0.94 (95% CI 0.83, 0.98), and specificity of 1.00 (95% CI 0.93, 1.00). Limitations include lack of sample suitability assessment, and need to validate these findings in additional patient populations. INTERPRETATION: This metabolomic approach has potential for diagnostic applications in infectious diseases testing, including other respiratory viruses, and may eventually be adapted for point-of-care testing. FUNDING: None.


Subject(s)
Influenza, Human/diagnosis , Machine Learning , Metabolome , Molecular Diagnostic Techniques/methods , Adolescent , Adult , Child , Child, Preschool , Female , Gas Chromatography-Mass Spectrometry/methods , Humans , Influenza, Human/metabolism , Influenza, Human/virology , Male , Metabolomics/methods , Nasal Mucosa/metabolism , Nasal Mucosa/virology , Orthomyxoviridae/pathogenicity , Pyrrolidonecarboxylic Acid/analysis
7.
Dis Markers ; 2021: 6803510, 2021.
Article in English | MEDLINE | ID: covidwho-1443673

ABSTRACT

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most significant public health threat worldwide. Patients with severe COVID-19 usually have pneumonia concomitant with local inflammation and sometimes a cytokine storm. Specific components of the SARS-CoV-2 virus trigger lung inflammation, and recruitment of immune cells to the lungs exacerbates this process, although much remains unknown about the pathogenesis of COVID-19. Our study of lung type II pneumocyte cells (A549) demonstrated that ORF7, an open reading frame (ORF) in the genome of SARS-CoV-2, induced the production of CCL2, a chemokine that promotes the chemotaxis of monocytes, and decreased the expression of IL-8, a chemokine that recruits neutrophils. A549 cells also had an increased level of IL-6. The results of our chemotaxis Transwell assay suggested that ORF7 augmented monocyte infiltration and reduced the number of neutrophils. We conclude that the ORF7 of SARS-CoV-2 may have specific effects on the immunological changes in tissues after infection. These results suggest that the functions of other ORFs of SARS-CoV-2 should also be comprehensively examined.


Subject(s)
COVID-19/metabolism , Chemotaxis , Monocytes/pathology , Neutrophils/pathology , Open Reading Frames/physiology , Pneumonia/pathology , Viral Proteins/metabolism , A549 Cells , Chemokine CCL2/metabolism , Humans , In Vitro Techniques , Monocytes/immunology , Monocytes/metabolism , Neutrophils/immunology , Neutrophils/metabolism , Pneumonia/immunology , Pneumonia/metabolism , SARS-CoV-2/metabolism , Viral Proteins/genetics
8.
J Clin Virol ; 127: 104383, 2020 06.
Article in English | MEDLINE | ID: covidwho-1385847

ABSTRACT

BACKGROUND: Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and there is a need to assess their test performance relative to one another. OBJECTIVES: The aim of this study was to compare the test performance of the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene. STUDY DESIGN: We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient. RESULTS: A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6. CONCLUSION: The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.


Subject(s)
Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Molecular Diagnostic Techniques/standards , Pneumonia, Viral/diagnosis , Reagent Kits, Diagnostic/standards , Viral Envelope Proteins/isolation & purification , Betacoronavirus/genetics , COVID-19 , Coronavirus Envelope Proteins , Humans , Nasopharynx/virology , Pandemics , Reproducibility of Results , SARS-CoV-2 , Viral Envelope Proteins/genetics
10.
EBioMedicine ; 67: 103355, 2021 May.
Article in English | MEDLINE | ID: covidwho-1385438

ABSTRACT

BACKGROUND: There is increasing concern that persistent infection of SARS-CoV-2 within immunocompromised hosts could serve as a reservoir for mutation accumulation and subsequent emergence of novel strains with the potential to evade immune responses. METHODS: We describe three patients with acute lymphoblastic leukemia who were persistently positive for SARS-CoV-2 by real-time polymerase chain reaction. Viral viability from longitudinally-collected specimens was assessed. Whole-genome sequencing and serological studies were performed to measure viral evolution and evidence of immune escape. FINDINGS: We found compelling evidence of ongoing replication and infectivity for up to 162 days from initial positive by subgenomic RNA, single-stranded RNA, and viral culture analysis. Our results reveal a broad spectrum of infectivity, host immune responses, and accumulation of mutations, some with the potential for immune escape. INTERPRETATION: Our results highlight the potential need to reassess infection control precautions in the management and care of immunocompromised patients. Routine surveillance of mutations and evaluation of their potential impact on viral transmission and immune escape should be considered.


Subject(s)
COVID-19/immunology , Immune Evasion , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/virology , SARS-CoV-2/genetics , COVID-19/virology , Child, Preschool , Evolution, Molecular , Female , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Immunity, Humoral , Male , Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology , SARS-CoV-2/classification , SARS-CoV-2/immunology , Sequence Analysis, RNA , Whole Genome Sequencing , Young Adult
11.
Diagn Microbiol Infect Dis ; 101(4): 115517, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1347571

ABSTRACT

Dengue and COVID-19 cocirculation presents a diagnostic conundrum for physicians evaluating patients with acute febrile illnesses, both in endemic regions and among returning travelers. We present a case of a returning traveler from Pakistan who, following repeated negative SARS-CoV-2 tests, was found to have a Dengue virus serotype 2 infection.


Subject(s)
COVID-19/diagnosis , Dengue/diagnosis , SARS-CoV-2 , Adult , COVID-19/epidemiology , California/epidemiology , Dengue/epidemiology , Dengue Virus/classification , Dengue Virus/genetics , Female , Genome, Viral , Humans , Pakistan/epidemiology , Phylogeny , Reverse Transcriptase Polymerase Chain Reaction , Serogroup , Travel
12.
Emerg Infect Dis ; 27(10): 2720-2723, 2021.
Article in English | MEDLINE | ID: covidwho-1323073

ABSTRACT

We report persistent severe acute respiratory syndrome coronavirus 2 infection in a patient with HIV/AIDS; the virus developed spike N terminal domain and receptor binding domain neutralization resistance mutations. Our findings suggest that immunocompromised patients can harbor emerging variants of severe acute respiratory syndrome coronavirus 2.


Subject(s)
Acquired Immunodeficiency Syndrome , COVID-19 , Humans , Mutation , Protein Binding , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
13.
J Clin Microbiol ; 59(8): e0085921, 2021 Jul 19.
Article in English | MEDLINE | ID: covidwho-1316925

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with concerning phenotypic mutations is of public health interest. Genomic surveillance is an important tool for a pandemic response, but many laboratories do not have the resources to support population-level sequencing. We hypothesized that a nucleic acid amplification test (NAAT) to genotype mutations in the viral spike protein could facilitate high-throughput variant surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase PCR (RT-qPCR) to detect three nonsynonymous spike protein mutations (L452R, E484K, N501Y). Assay specificity was validated with next-generation whole-genome sequencing. We then screened a large cohort of SARS-CoV-2-positive specimens from our San Francisco Bay Area population. Between 1 December 2020 and 1 March 2021, we screened 4,049 unique infections by genotyping RT-qPCR, with an assay failure rate of 2.8%. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K plus N501Y mutations. The assay had perfect (100%) concordance with whole-genome sequencing of a validation subset of 229 specimens and detected B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, and P.2 variants, among others. The assay revealed the rapid emergence of the L452R variant in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. We developed and clinically implemented a genotyping RT-qPCR to conduct high-throughput SARS-CoV-2 variant screening. This approach can be adapted for emerging mutations and immediately implemented in laboratories already performing NAAT worldwide using existing equipment, personnel, and extracted nucleic acid.


Subject(s)
COVID-19 , SARS-CoV-2 , Epidemiological Monitoring , Genotype , Humans , Reverse Transcriptase Polymerase Chain Reaction
14.
Biochem Mol Biol Educ ; 49(5): 720-728, 2021 09.
Article in English | MEDLINE | ID: covidwho-1263061

ABSTRACT

The COVID-19 pandemic is a huge challenge to education systems. Most governments around the world have temporarily closed schools, universities, and colleges. At the same time, teachers and students are encouraged to use the online and distance learning programs and platforms as an alternative. In the present study, we proposed a series of innovative solutions in Medical Molecular Biology education during the COVID-19 pandemic in China, including a flipped classroom model, live streaming course, chat Apps, and scientific papers on COVID-19 as additional learning material. Our results demonstrated that these innovations not only help teachers to maintain the teaching process as usual but also be useful for protecting students from psychological trauma. Our study indicates that online education with a well-designed workflow for conducting provides an alternative approach for teachers to maintain quality education during the onset of the emerging crisis.


Subject(s)
COVID-19/epidemiology , Curriculum , Education, Distance , Education, Medical , Mobile Applications , Molecular Biology/education , Pandemics , SARS-CoV-2 , China/epidemiology , Humans
15.
Clin Infect Dis ; 73(12): 2326-2328, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1172645

ABSTRACT

An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold <35, there was 95%-98% positive and 93%-96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Immunologic Tests , Prospective Studies , Retrospective Studies
16.
J Clin Virol ; 138: 104792, 2021 05.
Article in English | MEDLINE | ID: covidwho-1126921

ABSTRACT

BACKGROUND: Significant overlap exists between the symptoms of SARS-CoV-2 and other respiratory viruses. This poses a serious challenge to clinical diagnosis, laboratory testing, and infection control programs. OBJECTIVES: To evaluate the performance of the Hologic Panther Fusion Respiratory Assays (RA) compared to the GenMark ePlex Respiratory Pathogen Panel (RPP) and to assess the ability of the Panther Fusion to perform parallel testing of SARS-CoV-2 and other respiratory viruses from a single sample. STUDY DESIGN: A diagnostic comparison study was carried out using 375 clinical nasopharyngeal specimens. Assay performance was assessed by overall, positive, and negative percent agreement and Cohen's kappa coefficient. RESULTS: Overall agreement between the Fusion RA and ePlex RPP was 97.3 % (95 % CI 96.3-98.0), positive percent agreement was 97.2 % (95 % CI 93.0-99.2), negative percent agreement was 97.3 % (95 % CI 96.3-98.0), and the kappa coefficient was 0.85 (95 % CI 0.81-0.89). Forty additional viruses in 30 specimens were detected by Fusion that were not detected by ePlex. The maximum specimen throughput for parallel testing of the Fusion Respiratory Assays with SARS-CoV-2 was 275 samples in 20.7 h for Fusion SARS-CoV-2 and 350 samples in 20.0 h for Aptima Transcription Mediated Amplification SARS-CoV-2. CONCLUSION: Fusion RA demonstrated substantial agreement compared to the ePlex RPP. However, the Fusion detected respiratory viruses not identified by ePlex, consistent with higher clinical sensitivity. Workflows for parallel testing of respiratory pathogens and SARS-CoV-2 demonstrate that the Panther Fusion instrument provides a flexible, moderate to high throughput testing option for pandemic and seasonal respiratory viruses.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Nasopharynx/virology , RNA, Viral/isolation & purification , SARS-CoV-2/isolation & purification , Diagnostic Tests, Routine , Humans , Influenza, Human/diagnosis , Retrospective Studies , Sensitivity and Specificity
17.
Diagn Microbiol Infect Dis ; 100(3): 115365, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1116561

ABSTRACT

We present the case of an inpatient with pneumonia and repeatedly negative nasopharyngeal SARS-CoV-2 testing. In such challenging cases, alternative diagnostic options include lower respiratory tract and plasma SARS-CoV-2 RNA testing, of which the latter may be particularly useful where bronchoscopy is deferred due to clinical factors or transmission risk.


Subject(s)
COVID-19/diagnosis , Plasma/virology , SARS-CoV-2/isolation & purification , Adult , COVID-19 Nucleic Acid Testing , Humans , Male , Nasopharynx/virology , RNA, Viral/genetics , Specimen Handling
18.
Emerg Infect Dis ; 27(2): 632-635, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1048938

ABSTRACT

We developed an assay that detects minus-strand RNA as a surrogate for actively replicating severe acute respiratory syndrome coronavirus 2. We detected minus-strand RNA in 41 persons with coronavirus disease up to 30 days after symptom onset. This assay might inform clinical decision-making about patient infectiousness.


Subject(s)
COVID-19 Nucleic Acid Testing/standards , COVID-19/diagnosis , RNA, Viral/analysis , SARS-CoV-2/genetics , Virus Replication/genetics , Adult , COVID-19/transmission , COVID-19 Nucleic Acid Testing/methods , Clinical Decision-Making , Disease Transmission, Infectious , Feasibility Studies , Female , Humans , Male , Middle Aged , Prospective Studies , RNA, Viral/physiology , Retrospective Studies , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/physiology
19.
J Clin Microbiol ; 58(8)2020 Jul 23.
Article in English | MEDLINE | ID: covidwho-999209

ABSTRACT

Several point-of-care (POC) molecular tests have received emergency use authorization (EUA) from the Food and Drug Administration (FDA) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The test performance characteristics of the Accula (Mesa Biotech) SARS-CoV-2 POC test need to be evaluated to inform its optimal use. The aim of this study was to assess the test performance of the Accula SARS-CoV-2 test. The performance of the Accula test was assessed by comparing results of 100 nasopharyngeal swab samples previously characterized by the Stanford Health Care EUA laboratory-developed test (SHC-LDT), targeting the envelope (E) gene. Assay concordance was assessed by overall percent agreement, positive percent agreement (PPA), negative percent agreement (NPA), and Cohen's kappa coefficient. Overall percent agreement between the assays was 84.0% (95% confidence interval [CI], 75.3 to 90.6%), PPA was 68.0% (95% CI, 53.3 to 80.5%), and the kappa coefficient was 0.68 (95% CI, 0.54 to 0.82). Sixteen specimens detected by the SHC-LDT were not detected by the Accula test and showed low viral load burden, with a median cycle threshold value of 37.7. NPA was 100% (95% CI, 94.2 to 100%). Compared to the SHC-LDT, the Accula SARS-CoV-2 test showed excellent negative agreement. However, positive agreement was low for samples with low viral load. The false-negative rate of the Accula POC test calls for a more thorough evaluation of POC test performance characteristics in clinical settings and for confirmatory testing in individuals with moderate to high pretest probability of SARS-CoV-2 who test negative on Accula.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Point-of-Care Testing , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/genetics , COVID-19 , COVID-19 Testing , Child , Child, Preschool , Coronavirus Infections/virology , False Negative Reactions , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Nasopharynx/virology , Pandemics , Pneumonia, Viral/virology , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity , Young Adult
20.
Sci Immunol ; 5(54)2020 12 07.
Article in English | MEDLINE | ID: covidwho-963892

ABSTRACT

SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.


Subject(s)
Antibodies, Viral/immunology , COVID-19/immunology , Severity of Illness Index , Adult , Aged , Aged, 80 and over , Angiotensin-Converting Enzyme 2/blood , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/immunology , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , COVID-19/blood , COVID-19/genetics , Enzyme-Linked Immunosorbent Assay , Female , Humans , Male , Middle Aged , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/blood , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
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