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1.
N Engl J Med ; 385(16): 1474-1484, 2021 10 14.
Article in English | MEDLINE | ID: covidwho-1612234

ABSTRACT

BACKGROUND: Despite the high efficacy of the BNT162b2 messenger RNA vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), rare breakthrough infections have been reported, including infections among health care workers. Data are needed to characterize these infections and define correlates of breakthrough and infectivity. METHODS: At the largest medical center in Israel, we identified breakthrough infections by performing extensive evaluations of health care workers who were symptomatic (including mild symptoms) or had known infection exposure. These evaluations included epidemiologic investigations, repeat reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assays, antigen-detecting rapid diagnostic testing (Ag-RDT), serologic assays, and genomic sequencing. Correlates of breakthrough infection were assessed in a case-control analysis. We matched patients with breakthrough infection who had antibody titers obtained within a week before SARS-CoV-2 detection (peri-infection period) with four to five uninfected controls and used generalized estimating equations to predict the geometric mean titers among cases and controls and the ratio between the titers in the two groups. We also assessed the correlation between neutralizing antibody titers and N gene cycle threshold (Ct) values with respect to infectivity. RESULTS: Among 1497 fully vaccinated health care workers for whom RT-PCR data were available, 39 SARS-CoV-2 breakthrough infections were documented. Neutralizing antibody titers in case patients during the peri-infection period were lower than those in matched uninfected controls (case-to-control ratio, 0.361; 95% confidence interval, 0.165 to 0.787). Higher peri-infection neutralizing antibody titers were associated with lower infectivity (higher Ct values). Most breakthrough cases were mild or asymptomatic, although 19% had persistent symptoms (>6 weeks). The B.1.1.7 (alpha) variant was found in 85% of samples tested. A total of 74% of case patients had a high viral load (Ct value, <30) at some point during their infection; however, of these patients, only 17 (59%) had a positive result on concurrent Ag-RDT. No secondary infections were documented. CONCLUSIONS: Among fully vaccinated health care workers, the occurrence of breakthrough infections with SARS-CoV-2 was correlated with neutralizing antibody titers during the peri-infection period. Most breakthrough infections were mild or asymptomatic, although persistent symptoms did occur.


Subject(s)
COVID-19 Vaccines , COVID-19/epidemiology , Health Personnel/statistics & numerical data , Adult , Asymptomatic Diseases , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , Case-Control Studies , Female , Humans , Israel/epidemiology , Male , Middle Aged , Reverse Transcriptase Polymerase Chain Reaction , Treatment Failure
2.
Crit Care ; 26(1): 10, 2022 01 04.
Article in English | MEDLINE | ID: covidwho-1604921

ABSTRACT

BACKGROUND: Research on the duration of infectivity of ICU patients with COVID-19 has been sparse. Tests based on Reverse Transcriptase polymerase chain reaction (RT-PCR) detect both live virus and non-infectious viral RNA. We aimed to determine the duration of infectiousness based on viral culture of nasopharyngeal samples of patients with COVID-19. METHODS: Prospective observational study in adult intensive care units with a diagnosis of COVID-19 Pneumonia. Patients had repeated nasopharyngeal sampling performed after day 10 of ICU admission. Culture positive rate (based on viral culture on Vero cells in a level 4 lab) and Cycle threshold from RT-PCR were measured. RESULTS: Nine patients of the 108 samples (8.3%, 95% CI 3.9-15.2%) grew live virus at a median of 13 days (interquartile range 11-19) after their initial positive test. 74.1% of patients were RT-PCR positive but culture negative, and the remaining (17.6%) were RT-PCR and culture negative. Cycle threshold showed excellent ability to predict the presence of live virus, with a Ct < 25 with an AUC of 0.90 (95% CI 0.83-0.97, p < 0.001). The specificity of a Ct > 25 to predict negative viral culture was 100% (95% CI 70-100%). CONCLUSION: 8.3% of our ICU patients with COVID-19 grew live virus at a median of 13 days post-initial positive RT-PCR test. Severity of illness, use of mechanical ventilation, and time between tests did not predict the presence of live virus. Cycle threshold of > 25 had the best ability to determine the lack of live virus in these patents.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , COVID-19/therapy , COVID-19/virology , COVID-19 Nucleic Acid Testing , Critical Illness , Humans , Intensive Care Units , Nasopharynx/virology , Prospective Studies , SARS-CoV-2/isolation & purification
3.
Medicine (Baltimore) ; 100(52): e28470, 2021 Dec 30.
Article in English | MEDLINE | ID: covidwho-1592821

ABSTRACT

INTRODUCTION: The outbreak of novel coronavirus (severe acute respiratory syndrome coronavirus 2), which causes the coronavirus disease 2019 (COVID-19), is the most important current health problem. The number of patients is increasing worldwide. Pneumonia is the most life-threatening complication of the disease. Prolonged viral shedding in hematological patients with COVID-19 has been demonstrated; however, data on COVID-19 patients receiving anti-CD20 monoclonal antibody therapy are limited. Accordingly, focusing on humoral immunity, herein, we present 4 COVID-19 patients who were on anti-CD20 monoclonal antibody treatment and had prolonged pneumonia. PATIENT CONCERNS: Two of 4 patients were on rituximab and the other 2 were on obinutuzumab therapy. DIAGNOSIS: The polymerase chain reaction test results for severe acute respiratory syndrome coronavirus 2 were positive for all 4 patients and their COVID pneumonia lasted for >50 days. INTERVENTIONS: Although all patients were treated with an adequate amount of convalescent plasma, prolonged polymerase chain reaction positivity and prolonged pneumonia were possibly due to the lack of ability of the immune system to initiate its antibody response. OUTCOMES: Despite the administration of standard therapies, recurrent pneumonia observed in the present case series of non-neutropenic patients, in whom primary malignancies were under control. CONCLUSIONS: It is suggested that further investigations should be performed to understand the underlying pathophysiology.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Antibodies, Monoclonal/therapeutic use , Antineoplastic Agents, Immunological/therapeutic use , COVID-19/drug therapy , Pneumonia/epidemiology , Rituximab/therapeutic use , Adult , Aged , COVID-19/diagnosis , COVID-19/therapy , COVID-19 Nucleic Acid Testing , Female , Humans , Immunization, Passive , Middle Aged , Polymerase Chain Reaction , Recurrence , SARS-CoV-2 , Treatment Outcome
4.
Sci Rep ; 11(1): 23963, 2021 12 14.
Article in English | MEDLINE | ID: covidwho-1585798

ABSTRACT

We demonstrate that finite impulse response (FIR) models can be applied to analyze the time evolution of an epidemic with its impact on deaths and healthcare strain. Using time series data for COVID-19-related cases, ICU admissions and deaths from Sweden, the FIR model gives a consistent epidemiological trajectory for a simple delta filter function. This results in a consistent scaling between the time series if appropriate time delays are applied and allows the reconstruction of cases for times before July 2020, when RT-PCR testing was not widely available. Combined with randomized RT-PCR study results, we utilize this approach to estimate the total number of infections in Sweden, and the corresponding infection-to-fatality ratio (IFR), infection-to-case ratio (ICR), and infection-to-ICU admission ratio (IIAR). Our values for IFR, ICR and IIAR are essentially constant over large parts of 2020 in contrast with claims of healthcare adaptation or mutated virus variants importantly affecting these ratios. We observe a diminished IFR in late summer 2020 as well as a strong decline during 2021, following the launch of a nation-wide vaccination program. The total number of infections during 2020 is estimated to 1.3 million, indicating that Sweden was far from herd immunity.


Subject(s)
COVID-19/epidemiology , Mortality/trends , SARS-CoV-2/isolation & purification , COVID-19/mortality , COVID-19 Nucleic Acid Testing , Finite Element Analysis , Hospitalization/statistics & numerical data , Humans , Intensive Care Units , SARS-CoV-2/genetics , Sweden/epidemiology , Time Factors
5.
Sci Rep ; 11(1): 24234, 2021 12 20.
Article in English | MEDLINE | ID: covidwho-1585791

ABSTRACT

The main strategy for response and control of COVID-19 demands the use of rapid, accurate diagnostic tests aimed at the first point of health care. During the emergency, an increase in asymptomatic and symptomatic cases results in a great demand for molecular tests, which is promoting the development and application of rapid diagnostic technologies. In this study, we describe the development and evaluation of RT-LAMP to detect SARS-CoV-2 based on three genes (ORF1ab, M and N genes) in monoplex and triplex format. RT-LAMP assays were compared with the gold standard method RT-qPCR. The triplex format (RdRp, M and N genes) allowed obtaining comparable results with de RT-qPCR (RdRp and E genes), presented a sensitivity of 98.9% and a specificity of 97.9%, opening the opportunity to apply this method to detect SARS-CoV-2 at primary health-care centers.


Subject(s)
Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , RNA, Viral/metabolism , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , COVID-19/virology , COVID-19 Nucleic Acid Testing/methods , Coronavirus RNA-Dependent RNA Polymerase/genetics , Humans , Limit of Detection , Nasopharynx/virology , Nucleocapsid Proteins/genetics , Point-of-Care Systems , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Viral Matrix Proteins/genetics
6.
PLoS One ; 16(12): e0260884, 2021.
Article in English | MEDLINE | ID: covidwho-1581769

ABSTRACT

OBJECTIVES: To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/µL. METHODS: A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset. The model was then used to convert the stored cycle threshold values of a large dataset of 6208 diagnostic samples into copies/µL of SARS-CoV-2. The calculated viral load was used for a single cohort retrospective study. Finally, the cohort was randomly divided into a training set (n = 3095) and an evaluation set (n = 3113) to establish a logistic regression model for predicting case-fatality and to assess its accuracy. RESULTS: The model for converting the Ct values into copies/µL was suitably accurate. The calculated viral load over time in the cohort of Covid-19 positive samples showed very low viral loads during the summer inter-epidemic waves in Italy. The calculated viral load along with gender and age allowed building a predictive model of case-fatality probability which showed high specificity (99.0%) and low sensitivity (21.7%) at the optimal threshold which varied by modifying the threshold (i.e. 75% sensitivity and 83.7% specificity). Alternative models including categorised cVL or raw cycle thresholds obtained by the same diagnostic method also gave the same performance. CONCLUSION: The modelling of the cycle threshold values using digital PCR had the potential of fostering studies addressing issues regarding Sars-CoV-2; furthermore, it may allow setting up predictive tools capable of early identifying those patients at high risk of case-fatality already at diagnosis, irrespective of the diagnostic RT-qPCR platform in use. Depending upon the epidemiological situation, public health authority policies/aims, the resources available and the thresholds used, adequate sensitivity could be achieved with acceptable low specificity.


Subject(s)
COVID-19/virology , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Viral Load/methods , Adolescent , Adult , Aged , COVID-19/mortality , COVID-19 Nucleic Acid Testing/methods , Child , Child, Preschool , Female , Genome, Viral , Humans , Logistic Models , Male , Middle Aged , Retrospective Studies , Sensitivity and Specificity , Young Adult
7.
PLoS One ; 16(12): e0261230, 2021.
Article in English | MEDLINE | ID: covidwho-1581758

ABSTRACT

The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine/methods , Mass Screening/methods , Pandemics/prevention & control , Diagnostic Screening Programs , Humans , Universities
9.
Rev Med Virol ; 31(6): e2215, 2021 11.
Article in English | MEDLINE | ID: covidwho-1573992

ABSTRACT

The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective methodology. The advent of the loop-mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point-of-care test for the diagnosis of Covid-19 in endemic areas, especially for low- and middle-income countries.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Point-of-Care Testing/organization & administration , SARS-CoV-2/genetics , Bibliometrics , COVID-19/epidemiology , COVID-19/pathology , COVID-19/virology , COVID-19 Nucleic Acid Testing/economics , COVID-19 Nucleic Acid Testing/instrumentation , Humans , Molecular Diagnostic Techniques/economics , Molecular Diagnostic Techniques/instrumentation , Nucleic Acid Amplification Techniques/economics , Nucleic Acid Amplification Techniques/instrumentation , Point-of-Care Testing/economics , RNA, Viral/genetics , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
10.
Aging (Albany NY) ; 13(23): 24931-24942, 2021 12 12.
Article in English | MEDLINE | ID: covidwho-1573020

ABSTRACT

Since the Coronavirus 19 (COVID-19) pandemic, several SARS-CoV-2 variants of concern (SARS-CoV-2 VOC) have been reported. The B.1.1.7 variant has been associated with increased mortality and transmission risk. Furthermore, cluster and possible co-infection cases could occur in the next influenza season or COVID-19 pandemic wave, warranting efficient diagnosis and treatment decision making. Here, we aimed to detect SARS-CoV-2 and other common respiratory viruses using multiplex RT-PCR developed on the LabTurbo AIO 48 open system. We performed a multicenter study to evaluate the performance and analytical sensitivity of the LabTurbo AIO 48 system for SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) using 652 nasopharyngeal swab clinical samples from patients. The LabTurbo AIO 48 system demonstrated a sensitivity of 9.4 copies/per PCR for N2 of SARS-CoV-2; 24 copies/per PCR for M of influenza A and B; and 24 copies/per PCR for N of RSV. The assay presented consistent performance in the multicenter study. The multiplex RT-PCR applied on the LabTurbo AIO 48 open platform provided highly sensitive, robust, and accurate results and enabled high-throughput detection of B.1.1.7, influenza A/B, and RSV with short turnaround times. Therefore, this automated molecular diagnostic assay could enable streamlined testing if COVID-19 becomes a seasonal disease.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction/methods , Respiratory Syncytial Virus Infections/diagnosis , Adult , Aged , COVID-19/virology , Female , Humans , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza, Human/virology , Influenzavirus B/genetics , Influenzavirus B/isolation & purification , Male , Middle Aged , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Viruses/genetics , Respiratory Syncytial Viruses/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Young Adult
11.
Viruses ; 13(12)2021 12 10.
Article in English | MEDLINE | ID: covidwho-1572657

ABSTRACT

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/genetics , SARS-CoV-2/isolation & purification , Brazil/epidemiology , COVID-19/epidemiology , Coronavirus RNA-Dependent RNA Polymerase/genetics , DNA Primers , False Negative Reactions , Genome, Viral/genetics , Humans , Mutation , Phosphoproteins/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics
12.
Nagoya J Med Sci ; 83(4): 883-891, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1562255

ABSTRACT

A 76-year-old woman was admitted to the emergency room of Nagano Municipal Hospital with the complain of severe back pain. Chest and abdominal enhanced computed tomography scans showed bilateral adrenal infarction and minute pulmonary nodules, but she had no respiratory symptoms. After admission, a family member of the patient was found to have been in close contact with a coronavirus disease 2019 (COVID-19) patient. Thus, polymerase chain reaction and antigen tests of severe acute respiratory syndrome coronavirus 2 were conducted, and both tests returned positive. D-dimer levels were normal on admission but increased 2 days thereafter. Anticoagulation therapy and steroid replacement were started, and the patient improved over about two weeks. One month after the onset of adrenal infarction, a rapid adrenocorticotropic hormone loading test was conducted, which revealed that the primary adrenal insufficiency due to adrenal infarction might have been caused by the COVID-19 infection. This case was rare and suggestive of adrenal infarction with COVID-19, which usually presents at the severe stage. In patients with COVID-19, attention should be paid to the onset of thrombosis, even with mild respiratory infection. We also suggest that patients with thrombosis should be suspected of having COVID-19 even in the absence of respiratory infectious symptoms in a situation of COVID-19 epidemic.


Subject(s)
Adrenal Glands/blood supply , COVID-19/complications , Infarction , Thrombosis/etiology , Aged , COVID-19/blood , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing , Female , Humans , Infarction/etiology , Respiratory Tract Infections , SARS-CoV-2/isolation & purification
13.
Int J Cancer ; 150(3): 431-439, 2022 Feb 01.
Article in English | MEDLINE | ID: covidwho-1561555

ABSTRACT

We retrospectively analyzed the epidemiological characteristics of cancer patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and their correlations with publicly available mobility data. Between 19 October 2020 and 28 February 2021, 4754 patient visits were carried out, and 1454 treatments have been applied at the Haemato-Oncology Day Hospital Merano. Additional measures to prevent local SARS-CoV-2 transmission included a specific questionnaire for coronavirus disease 2019 (COVID-19) symptoms as well as a SARS-CoV-2 real-time polymerase-chain reaction (RT-PCR) 2 days prior to any intravenous or subcutaneous therapy. Community mobility was assessed through publicly available mobile phone tracking data from Google; 106/719 (14.7%) cancer patients have been tested positive for SARS-CoV-2 by PCR during the second wave compared to 5/640 (0.8%) within the first wave (P < .001); 66/106 (62%) had solid tumors, and 40/106 (38%) had hematological malignancies; 90/106 (85%) patients received ongoing antitumor therapies. Mortality rate of COVID-19 positive cancer patients (7/106; 6.6%) was higher compared to the overall population (731/46 421; 1.6%; P < .001). Strict control measures at our department led to a significantly lower test positivity rate compared to the general population, resulting in a reduction of 58.5% of new SARS-CoV-2 cases. Over time, infection rates and community mobility correlated in the first and second wave after initiating and lifting restrictions. Our findings underscore the importance of strict preventive control measures including testing and contact tracing in vulnerable subpopulations such as cancer patients, particularly if social restriction policies are being lifted. Smartphone-based mobility data may help to guide policy makers to prevent a vulnerable population like cancer patients from virus transmission.


Subject(s)
COVID-19/diagnosis , Mandatory Programs , Neoplasms/complications , Quarantine , SARS-CoV-2/isolation & purification , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Female , Humans , Italy/epidemiology , Male , Middle Aged , Neoplasms/epidemiology , Neoplasms/virology , Pandemics , Retrospective Studies , SARS-CoV-2/genetics , Travel
14.
Viruses ; 13(12)2021 12 02.
Article in English | MEDLINE | ID: covidwho-1554951

ABSTRACT

During COVID-19 pandemics, the availability of testing has often been a limiting factor during patient admissions into the hospital. To circumvent this problem, we adapted an existing diagnostic assay, Seegene Allplex SARS-CoV-2, into a point-of-care-style direct qPCR (POC dqPCR) assay and implemented it in the Emergency Department of Clinical Hospital Center Rijeka, Croatia. In a 4-month analysis, we tested over 10,000 patients and demonstrated that POC-dqPCR is robust and reliable and can be successfully implemented in emergency departments and similar near-patient settings and can be performed by medical personnel with little prior experience in qPCR.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Emergency Service, Hospital , Point-of-Care Testing , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , Croatia/epidemiology , Humans , RNA, Viral/genetics , Reproducibility of Results , SARS-CoV-2/genetics , Sensitivity and Specificity
15.
J Nippon Med Sch ; 88(4): 380-383, 2021 Sep 01.
Article in English | MEDLINE | ID: covidwho-1551292

ABSTRACT

We assessed the association of severity of coronavirus disease 2019 (COVID-19) with acute respiratory syndrome coronavirus 2 (SARS-CoV-2) load, IgG antibody level, and prognostic indicators.Twenty-one patients hospitalized with COVID-19 were classified as having severe or mild disease on the basis of average respiratory rate during hospitalization (severe: ≥22 breaths/min; mild: <22 breaths/min). Viral load in nasopharyngeal samples, blood levels of C-reactive protein (CRP), lymphocytes, and D-dimer on admission and plasma immunoglobulin G (IgG) index on Day 7±2 after symptom onset were compared in relation to disease severity. Seven patients had severe disease and 14 had mild disease. Those with severe disease had a significantly higher IgG index (median: 3.75 vs 0.56, p=0.01) and CRP (median: 8.6 vs 1.0 mg/dL, p<0.001) and D-dimer levels (median: 1.65 vs 0.75 µg/mL; p=0.002) and a significantly lower lymphocyte count (median: 1,176 vs 666 cells/µL, p=0.005) and viral load (median: 8.7×106 vs 2.3×104 copies/mL, p=0.005). Furthermore, time from symptom onset to virus disappearance was significantly longer in severe patients (median: 24 vs 17 days, p=0.03). A high IgG index in the early phase of the disease was associated with severe disease and might serve as a prognostic indicator.


Subject(s)
Antibodies, Viral/blood , COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing , COVID-19/diagnosis , Immunoglobulin G/blood , SARS-CoV-2/pathogenicity , Viral Load , Adult , Aged , Biomarkers/blood , COVID-19/blood , COVID-19/drug therapy , COVID-19/therapy , COVID-19/virology , Female , Hospitalization , Host-Pathogen Interactions , Humans , Japan , Male , Middle Aged , Oxygen Inhalation Therapy , Predictive Value of Tests , Prognosis , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Severity of Illness Index , Time Factors
16.
Biomed Pharmacother ; 144: 112353, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1544808

ABSTRACT

Almost 80% of people confronting COVID-19 recover from COVID-19 disease without any particular treatments. They experience heterogeneous symptoms; a wide range of respiratory symptoms, cough, dyspnea, fever, and viral pneumonia. However, some others need urgent intervention and special treatment to get rid of this widespread disease. So far, there isn't any unique drug for the potential treatment of COVID 19. However, some available therapeutic drugs used for other diseases seem beneficial for the COVID-19 treatment. On the other hand, there is a robust global concern for developing an efficient COVID-19 vaccine to control the COVID-19 pandemic sustainably. According to the WHO report, since 8 October 2021, 320 vaccines have been in progress. 194 vaccines are in the pre-clinical development stage that 126 of them are in clinical progression. Here, in this paper, we have comprehensively reviewed the most recent and updated information about coronavirus and its mutations, all the potential therapeutic approaches for treating COVID-19, developed diagnostic systems for COVID- 19 and the available COVID-19 vaccines and their mechanism of action.


Subject(s)
COVID-19 Vaccines/therapeutic use , COVID-19/drug therapy , COVID-19/prevention & control , Biosensing Techniques/methods , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing/methods , Dexamethasone/therapeutic use , Glucocorticoids/therapeutic use , Humans , Molecular Diagnostic Techniques/methods , Mutation , Nucleic Acid Amplification Techniques/methods , Point-of-Care Testing , SARS-CoV-2/genetics , World Health Organization
17.
J Med Virol ; 93(12): 6837-6840, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544319

ABSTRACT

BACKGROUND: Gargle samples have been proposed as a noninvasive method for detection of SARS-CoV-2 RNA. The clinical performance of gargle specimens diluted in Cobas® PCR Media and in Cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS-CoV-2 RNA. STUDY DESIGN: Participants were recruited prospectively in two COVID-19 screening clinics. In addition to the ONPS, participants gargled with 5 ml of natural spring water split in the laboratory as follows: 1 ml was added to 4.3 ml of polymerase chain reaction (PCR) media and 400 µl was added to 200 µl of lysis buffer. Testing was performed with the Cobas® SARS-CoV-2 test on the Cobas® 6800 or 8800 platforms. RESULTS: Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle test was positive. ONPS had, respectively, a sensitivity of 96.3% (95% confidence interval [CI]: 91.3-98.5); both gargle processing methods were slightly less but equally sensitive (90.3% [95% CI: 83.9-94.3]). When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct ) was significantly higher for gargles, suggesting lower viral loads. CONCLUSION: Gargle specimens directly added in PCR Media provide a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/genetics , Diagnostic Tests, Routine/methods , Humans , Mass Screening/methods , Prospective Studies , RNA, Viral/genetics , Saliva/virology , Specimen Handling/methods , Viral Load/genetics
18.
J Med Virol ; 93(12): 6803-6807, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544308

ABSTRACT

We evaluated the Panbio™ COVID-19 Ag Rapid Test Device as a point-of-care diagnostic tool for COVID-19 in 357 patients at a pediatric emergency department. Thirty-four patients tested positive by reverse transcription polymerase chain reaction, of which 24 were positive by the antigen assay. The sensitivity and specificity of the assay were 70.5% and 100%, respectively.


Subject(s)
Antigens, Viral/immunology , COVID-19/diagnosis , COVID-19/immunology , SARS-CoV-2/immunology , COVID-19 Nucleic Acid Testing/methods , COVID-19 Serological Testing/methods , Child , Child, Preschool , Emergency Service, Hospital , Female , Humans , Immunologic Tests/methods , Infant , Male , Nasopharynx/immunology , Nasopharynx/virology , Point-of-Care Testing , Prospective Studies , Sensitivity and Specificity
19.
JAMA ; 326(19): 1930-1939, 2021 11 16.
Article in English | MEDLINE | ID: covidwho-1544170

ABSTRACT

Importance: The effect of prior SARS-CoV-2 infection on vaccine protection remains poorly understood. Objective: To assess protection from SARS-CoV-2 breakthrough infection after mRNA vaccination among persons with vs without prior SARS-CoV-2 infection. Design, Setting, and Participants: Matched-cohort studies in Qatar for the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines. A total of 1 531 736 individuals vaccinated with either vaccine between December 21, 2020, and September 19, 2021, were followed up beginning 14 days after receiving the second dose until September 19, 2021. Exposures: Prior SARS-CoV-2 infection and COVID-19 vaccination. Main Outcomes and Measures: Incident SARS-CoV-2 infection, defined as a polymerase chain reaction (PCR)-positive nasopharyngeal swab regardless of reason for PCR testing or presence of symptoms. Cumulative incidence was calculated using the Kaplan-Meier estimator method. Results: The BNT162b2-vaccinated cohort comprised 99 226 individuals with and 290 432 matched individuals without prior PCR-confirmed infection (median age, 37 years; 68% male). The mRNA-1273-vaccinated cohort comprised 58 096 individuals with and 169 514 matched individuals without prior PCR-confirmed infection (median age, 36 years; 73% male). Among BNT162b2-vaccinated persons, 159 reinfections occurred in those with and 2509 in those without prior infection 14 days or more after dose 2. Among mRNA-1273-vaccinated persons, 43 reinfections occurred in those with and 368 infections in those without prior infection. Cumulative infection incidence among BNT162b2-vaccinated individuals was an estimated 0.15% (95% CI, 0.12%-0.18%) in those with and 0.83% (95% CI, 0.79%-0.87%) in those without prior infection at 120 days of follow-up (adjusted hazard ratio for breakthrough infection with prior infection, 0.18 [95% CI, 0.15-0.21]; P < .001). Cumulative infection incidence among mRNA-1273-vaccinated individuals was an estimated 0.11% (95% CI, 0.08%-0.15%) in those with and 0.35% (95% CI, 0.32%-0.40%) in those without prior infection at 120 days of follow-up (adjusted hazard ratio, 0.35 [95% CI, 0.25-0.48]; P < .001). Vaccinated individuals with prior infection 6 months or more before dose 1 had statistically significantly lower risk for breakthrough infection than those vaccinated less than 6 months before dose 1 (adjusted hazard ratio, 0.62 [95% CI, 0.42-0.92]; P = .02 for BNT162b2 and 0.40 [95% CI, 0.18-0.91]; P = .03 for mRNA-1273 vaccination). Conclusions and Relevance: Prior SARS-CoV-2 infection was associated with a statistically significantly lower risk for breakthrough infection among individuals receiving the BNT162b2 or mRNA-1273 vaccines in Qatar between December 21, 2020, and September 19, 2021. The observational study design precludes direct comparisons of infection risk between the 2 vaccines.


Subject(s)
COVID-19 Vaccines , COVID-19/complications , Adult , Aged , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , Cohort Studies , Female , Humans , Male , Middle Aged , Qatar
20.
J Med Virol ; 94(1): 240-245, 2022 01.
Article in English | MEDLINE | ID: covidwho-1544340

ABSTRACT

Many countries in the world are experiencing a recent surge in COVID-19 cases. This is mainly attributed to the emergence of new SARS-CoV-2 variants. Genome sequencing is the only means to detect the evolving virus mutants and emerging variants. Cycle threshold values have an inverse relationship with viral load and lower Ct values are also found to be associated with increased infectivity. In this study, we propose to use Ct values as an early indicator for upcoming COVID-19 waves. A retrospective cross-sectional study was carried out to analyze the Ct values of positive samples reported during the first wave and second wave (April 2020-May 2021). Median Ct values of confirmatory genes were taken into consideration for comparison. Ct values below 25, >25-30, and >30 were categorized as high, moderate, and low viral load respectively. Our study found a significantly higher proportion of positive samples with a low Ct value (<25) across age groups and gender during the second wave of the COVID-19 pandemic. A higher proportion of positive samples with a low Ct value (high viral load) may act as an early indicator of an upcoming surge.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , COVID-19/epidemiology , Adolescent , Adult , Asymptomatic Infections/epidemiology , COVID-19/virology , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Infant , Male , Middle Aged , Retrospective Studies , SARS-CoV-2/physiology , Viral Load , Young Adult
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