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1.
J Med Virol ; 93(8): 4748-4755, 2021 08.
Article in English | MEDLINE | ID: covidwho-1610624

ABSTRACT

Respiratory infections are one of the most frequent reasons for medical consultations in children. In low resource settings such as in Lao People's Democratic Republic, knowledge gaps and the dearth of laboratory capacity to support differential diagnosis may contribute to antibiotic overuse. We studied the etiology, temporal trends, and genetic diversity of viral respiratory infections in children to provide evidence for prevention and treatment guidelines. From September 2014 to October 2015, throat swabs and nasopharyngeal aspirates from 445 children under 10 years old with symptoms of acute respiratory infection were collected at the Children Hospital in Vientiane. Rapid antigen tests were performed for influenza A and B and respiratory syncytial virus. Real-time reverse-transcription polymerase chain reactions (RT-PCRs) were performed to detect 16 viruses. Influenza infections were detected with a higher sensitivity using PCR than with the rapid antigen test. By RT-PCR screening, at least one pathogen could be identified for 71.7% of cases. Human rhinoviruses were most frequently detected (29.9%), followed by influenza A and B viruses combined (15.9%). We identify and discuss the seasonality of some of the infections. Altogether these data provide a detailed characterization of respiratory pathogens in Lao children and we provide recommendations for vaccination and further studies.


Subject(s)
Coinfection/epidemiology , Respiratory Tract Infections/epidemiology , Virus Diseases/epidemiology , Viruses/genetics , Acute Disease/epidemiology , Child , Child, Preschool , Coinfection/virology , Female , Humans , Infant , Infant, Newborn , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/virology , Laos/epidemiology , Male , Prevalence , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/virology , Viruses/classification , Viruses/isolation & purification
2.
Clin Infect Dis ; 73(11): e3884-e3899, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1561131

ABSTRACT

BACKGROUND: We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset. METHODS: We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool. RESULTS: We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for >14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens. CONCLUSIONS: Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential.


Subject(s)
COVID-19 , Humans , Prospective Studies , RNA, Viral , Reproducibility of Results , SARS-CoV-2 , Serologic Tests
3.
J Endocrinol Invest ; 44(12): 2675-2684, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1504521

ABSTRACT

PURPOSE: Due to relevant repercussions on reproductive medicine, we aimed to evaluate feasibility of RT-PCR as a detection method of SARS-CoV-2 RNA in seminal fluid. METHODS: A qualitative determination of the RT-PCR assays in semen was performed through different approaches: (1) efficiency of RNA extraction from sperm and seminal plasma was determined using PRM1 and PRM2 mRNA and a heterologous system as control; (2) samples obtained by diluting viral preparation from a SARS-CoV-2 panel (virus cultured in Vero E6 cell lines) were tested; (3) viral presence in different fractions of seminal fluid (whole sample, seminal plasma and post-centrifugation pellet) was evaluated. Semen samples from mild and recovered COVID-19 subjects were collected by patients referring to the Infectious Disease Department of the Policlinico Umberto I Hospital - "Sapienza" University of Rome. Control subjects were recruited at the Laboratory of Seminology-Sperm Bank "Loredana Gandini'' of the same hospital. RESULTS: The control panel using viral preparations diluted in saline and seminal fluid showed the capability to detect viral RNA presence with Ct values depending on the initial viral concentration. All tested semen samples were negative for SARS-CoV-2, regardless of the nasopharyngeal swab result or seminal fluid fraction. CONCLUSION: These preliminary data show that RT-PCR for SARS-CoV-2 RNA testing appears to be a feasible method for the molecular diagnosis of SARS-CoV-2 in seminal fluid, supported by results of the control panel. The ability to detect SARS-CoV-2 in semen is extremely important for reproductive medicine, especially in assisted reproductive technology and sperm cryopreservation.


Subject(s)
COVID-19/diagnosis , Pathology, Molecular/methods , Semen/virology , Adult , Animals , Chlorocebus aethiops , Feasibility Studies , Humans , Male , RNA, Messenger/chemistry , RNA, Viral/chemistry , Real-Time Polymerase Chain Reaction , Reproductive Techniques , Vero Cells
4.
mSystems ; 6(2)2021 Apr 13.
Article in English | MEDLINE | ID: covidwho-1394062

ABSTRACT

Ongoing disease surveillance is a critical tool to mitigate viral outbreaks, especially during a pandemic. Environmental monitoring has significant promise even following widespread vaccination among high-risk populations. The goal of this work is to demonstrate molecular severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring in bulk floor dust and related samples as a proof of concept of a noninvasive environmental surveillance methodology for coronavirus disease 2019 (COVID-19) and potentially other viral diseases. Surface swab, passive sampler, and bulk floor dust samples were collected from the rooms of individuals positive for COVID-19, and SARS-CoV-2 was measured with quantitative reverse transcription-PCR (RT-qPCR) and two digital PCR (dPCR) methods. Bulk dust samples had a geometric mean concentration of 163 copies/mg of dust and ranged from nondetects to 23,049 copies/mg of dust detected using droplet digital PCR (ddPCR). An average of 89% of bulk dust samples were positive for the virus by the detection methods compared to 55% of surface swabs and fewer on the passive sampler (19% carpet, 29% polystyrene). In bulk dust, SARS-CoV-2 was detected in 76%, 93%, and 97% of samples measured by qPCR, chip-based dPCR, and droplet dPCR, respectively. Detectable viral RNA in the bulk vacuum bags did not measurably decay over 4 weeks, despite the application of a disinfectant before room cleaning. Future monitoring efforts should further evaluate RNA persistence and heterogeneity in dust. This study did not measure virus infectivity in dust or potential transmission associated with dust. Overall, this work demonstrates that bulk floor dust is a potentially useful matrix for long-term monitoring of viral disease in high-risk populations and buildings.IMPORTANCE Environmental surveillance to assess pathogen presence within a community is proving to be a critical tool to protect public health, and it is especially relevant during the ongoing COVID-19 pandemic. Importantly, environmental surveillance tools also allow for the detection of asymptomatic disease carriers and for routine monitoring of a large number of people as has been shown for SARS-CoV-2 wastewater monitoring. However, additional monitoring techniques are needed to screen for outbreaks in high-risk settings such as congregate care facilities. Here, we demonstrate that SARS-CoV-2 can be detected in bulk floor dust collected from rooms housing infected individuals. This analysis suggests that dust may be a useful and efficient matrix for routine surveillance of viral disease.

5.
Rev Esp Quimioter ; 33(6): 444-447, 2020 Dec.
Article in Spanish | MEDLINE | ID: covidwho-1390020

ABSTRACT

OBJECTIVE: Co-circulation of the two Influenza B lineages hinders forecast of strain to include in trivalent vaccine. Autonomous Communities such as Cantabria continue without supplying tetravalent vaccine. The aim of this study was to analyse epidemiological characteristics of influenza type B in Cantabria (2019-2020 season) as well as to establish the predominant lineage and its relation to the recommended vaccine. METHODS: Retrospective study whereby flu diagnosis and lineage analysis were determined by RT-PCR. RESULTS: All samples belonged to the Victoria lineage. Most prevalent viral co-infection was due to SARS-CoV-2. The population affected by influenza B was mainly paediatric and non-vaccinated patients more frequently required hospital admittance. CONCLUSIONS: Influenza type B has a higher incidence in the paediatric population and type A affects more the adult population. Only 28.8% of patients with Influenza B that presented with some underlying condition or risk factor were vaccinated. This shows the need to increase coverage with tetravalent vaccines in order to reduce the burden of disease associated with the Influenza B virus.


Subject(s)
COVID-19/epidemiology , Influenza B virus , Influenza, Human/epidemiology , Pandemics , SARS-CoV-2 , Adult , COVID-19/virology , Chi-Square Distribution , Child , Coinfection/epidemiology , Coinfection/virology , Epidemics , Female , Hospitalization/statistics & numerical data , Humans , Influenza Vaccines/administration & dosage , Influenza, Human/prevention & control , Influenza, Human/virology , Male , Retrospective Studies , Seasons , Spain/epidemiology , Statistics, Nonparametric
6.
Chemistry ; 26(52): 11950-11954, 2020 Sep 16.
Article in English | MEDLINE | ID: covidwho-1384141

ABSTRACT

Thymidine triphosphate bearing benzylidene-tetrahydroxanthylium near-IR fluorophore linked to the 5-methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348-times) presumably due to interactions in major groove and the fluorescence further increases in the single-stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light-up building block in real-time PCR for detection of SARS-CoV-2 virus.


Subject(s)
COVID-19 , DNA Replication , DNA Probes , Humans , Nucleotides , SARS-CoV-2
7.
Clin Chem ; 66(10): 1349-1350, 2020 10 01.
Article in English | MEDLINE | ID: covidwho-1383204

Subject(s)
COVID-19 , Humans , SARS-CoV-2
8.
J Med Virol ; 2020 Jun 30.
Article in English | MEDLINE | ID: covidwho-1381917

ABSTRACT

Palatine tonsils have been observed to harbor several distinct respiratory and herpesviruses in separate studies. In this study, the presence of these viruses in palatine tonsils was comprehensively studied in both children and adults. A cross-sectional analysis of 181 patients (median age 22 years; range, 2.6-66) operated for a benign tonsillar disease was conducted. Real-time polymerase chain reaction was performed to detect 27 distinct viruses in all: eight human herpesviruses, 16 respiratory viruses, parvo B19, and polyoma BK/JC viruses. Clinical characteristics of the patients and underlying conditions were evaluated. In total, 92% of patients had virus detected in tonsils (Epstein-Barr virus 72%, human herpesvirus 7, and 6B 54% and 16%, respectively, enterovirus 18%, parvovirus B19 7% and the rest <4%). No herpes simplex virus 2, varicella zoster virus, polyoma JC virus, parainfluenza-, metapneumo-, or coronaviruses were found. Enterovirus was more common in children and was frequently observed in the presence of HHV6B. None of the viruses showed a positive association to the tonsillar disease. Respiratory symptoms were not associated with the prevalence of viruses. This study comprehensively reports a cross-sectional view of intratonsillar virus infections in elective tonsillectomy patients in a wide age range cohort. Tonsils are a major virus reservoir for distinct herpes and respiratory viruses without a positive association with tonsillar disease or respiratory symptoms.

10.
J Perinat Med ; 49(6): 717-722, 2021 Jul 27.
Article in English | MEDLINE | ID: covidwho-1344175

ABSTRACT

OBJECTIVES: This study aims to detect the SARS-CoV-2 infection prevalence in asymptomatic pregnant women. METHODS: A group of 195 asymptomatic pregnant women who attended the prenatal care outclinic and to the obstetric emergency department was tested concomitantly for SARS-CoV-2 by RT-PCR and serological tests. RESULTS: The virus was detected by RT-PCR in two (1.02%) cases and 17 (8.71%) patients had antibodies detected by immunochromatographic tests. CONCLUSIONS: Due to the high risk of this emerging infection in the health of pregnant women, fetuses and newborns, we suggest the universal screening of all pregnant women admitted to hospital through the combined method RT-PCR and serological.


Subject(s)
Asymptomatic Infections/epidemiology , COVID-19/epidemiology , Pregnancy Complications, Infectious/epidemiology , Adult , Brazil/epidemiology , COVID-19/diagnosis , COVID-19/immunology , Cohort Studies , Female , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Middle Aged , Pregnancy , Pregnancy Complications, Infectious/diagnosis , Pregnancy Complications, Infectious/immunology , SARS-CoV-2/immunology , Young Adult
11.
J Perinat Med ; 49(6): 709-716, 2021 Jul 27.
Article in English | MEDLINE | ID: covidwho-1327988

ABSTRACT

OBJECTIVES: The Severe Acute Respiratory Distress Corona Virus 2 (SARS-CoV-2) pandemic poses special challenges for the society and especially the medical staff. Even if a rather mild course is assumed among pregnant women the measures to prevent transmission of the infection are of outstanding importance. METHODS: To screen asymptomatic pregnant women during admission to our university maternal hospital we focused on anti-SARS-CoV-2-specific IgG and IgA antibody responses. Hundred and fifty one women admitted to the hospital for childbirth or caesarean delivery were included. In case of suspicious anti-SARS-CoV-2-antibody levels an RT-PCR was performed to confirm an ongoing infection with SARS-CoV-2. RESULTS: A total of 89% showed negative results for anti-SARS-CoV-2-IgA antibodies, whereas 3% were borderline and 7% positive (both labeled as suspicious). In only one patient with suspicious serology we detected SARS-CoV-2-RNA in the following RT-PCR. 2% presented anti-SARS-CoV-2-IgG antibodies, all being positive for anti-SARS-CoV-2-IgA. The observed positive rate of our study collective of 10.6% seemed much higher than the expected one (1.3%) based on the reports of the Robert Koch Institute and the specifications given by the test's manufacturer. The expected positive predictive value (PPV) was 4.3-6.7 times higher than the observed one. CONCLUSIONS: To our knowledge this is the first report of anti-SARS-CoV-2-antibody levels in the peripartum period of asymptomatic women. As the positive anti-SARS-CoV-2 serology poorly correlated with the confirmatory RT-PCR and the fact that mainly the detection of the virus by PCR correlates with the patient's infectiousness we suggest to rather perform a SARS-CoV-2-PCR-based admission screening in perinatal centers to prevent the spread of the disease.


Subject(s)
Asymptomatic Infections , COVID-19/diagnosis , Pregnancy Complications, Infectious/diagnosis , SARS-CoV-2/immunology , Adolescent , Adult , COVID-19/immunology , Female , Humans , Immunoglobulin A/blood , Immunoglobulin G/blood , Middle Aged , Predictive Value of Tests , Pregnancy , Pregnancy Complications, Infectious/immunology , Retrospective Studies , Young Adult
12.
Clin Microbiol Infect ; 27(10): 1520.e7-1520.e10, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1297038

ABSTRACT

OBJECTIVES: Dexamethasone has become the standard of care for severe coronavirus disease 2019 (COVID-19), but its virological impact is poorly understood. The objectives of this work were to characterize the kinetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) concentration in the upper respiratory tract (URT) and the antibody response in patients with (D+) and without (D-) dexamethasone treatment. METHODS: Data and biosamples from hospitalized patients with severe COVID-19, enrolled between 4th March and 11th December 2020 in a prospective observational study, were analysed. SARS-CoV-2 virus concentration in serial URT samples was measured using RT-PCR. SARS-CoV-2-specific immunoglobulins A and G (IgA and IgG) were measured in serum samples using S1-ELISA. RESULTS: We compared 101 immunocompetent patients who received dexamethasone (according to the inclusion criteria and dosage determined in the RECOVERY trial) to 93 immunocompetent patients with comparable disease severity from the first months of the pandemic, who had not been treated with dexamethasone or other glucocorticoids. We found no inter-group differences in virus concentration kinetics, duration of presence of viral loads >106 viral copies/mL (D+ median 17 days (IQR 13-24), D- 19 days (IQR 13-29)), or time from symptom onset until seroconversion (IgA: D+ median 11.5 days (IQR 11-12), D- 14 days (IQR 11.5-15.75); IgG: D+ 13 days (IQR 12-14.5), D- 12 days (IQR 11-15)). CONCLUSION: Dexamethasone does not appear to lead to a change in virus clearance or a delay in antibody response in immunocompetent patients hospitalized with severe COVID-19.


Subject(s)
Antibodies, Viral/blood , COVID-19/drug therapy , Dexamethasone/therapeutic use , SARS-CoV-2/isolation & purification , Anti-Inflammatory Agents/therapeutic use , COVID-19/blood , COVID-19/immunology , COVID-19/virology , Hospitalization , Humans , Immunoglobulin A/blood , Immunoglobulin G/blood , Kinetics , Prospective Studies , RNA, Viral/analysis , Respiratory System/virology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Seroconversion , Viral Load
13.
J Clin Microbiol ; 59(7): e0043121, 2021 06 18.
Article in English | MEDLINE | ID: covidwho-1276888

ABSTRACT

Patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be diagnosed by PCR during acute infection or later in their clinical course by detection of virus-specific antibodies. While in theory complementary, both PCR and serologic tests have practical shortcomings. A retrospective study was performed in order to further define these limitations in a clinical context and to determine how to best utilize these tests in a coherent fashion. A total of 3,075 patients underwent both PCR and serology tests at University of California, Los Angeles (UCLA), in the study period. Among these, 2,731 (89%) had no positive tests at all, 73 (2%) had a positive PCR test and only negative serology tests, 144 (5%) had a positive serology test and only negative PCR tests, and 127 (4%) had positive PCR and serology tests. Approximately half of the patients with discordant results (i.e., PCR positive and serology negative or vice versa) had mistimed tests in reference to the course of their disease. PCR-positive patients who were asymptomatic or pregnant were less likely to generate a detectable humoral immune response to SARS-CoV-2. On a quantitative level, the log number of days between symptom onset and PCR test was positively correlated with cycle threshold (CT) values. However, there was no apparent relationship between PCR CT and serologic (arbitrary units per milliliter) results.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Humans , Los Angeles , Polymerase Chain Reaction , Retrospective Studies , Serologic Tests
14.
J Med Virol ; 93(9): 5588-5593, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1272208

ABSTRACT

Reverse transcription fluorescence resonance energy transfer-polymerase chain reaction (FRET-PCRs) were designed against the two most common mutations in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (A23403G in the spike protein; C14408T in the RNA-dependent RNA polymerase). Based on high-resolution melting curve analysis, the reverse transcription (RT) FRET-PCRs identified the mutations in american type culture collection control viruses, and feline and human clinical samples. All major makes of PCR machines can perform melting curve analysis and thus further specifically designed FRET-PCRs could enable active surveillance for mutations and variants in countries where genome sequencing is not readily available.


Subject(s)
COVID-19 Serological Testing/methods , Polymerase Chain Reaction , RNA-Dependent RNA Polymerase , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Animals , COVID-19/diagnosis , COVID-19/virology , Cats , Coronavirus RNA-Dependent RNA Polymerase/analysis , Coronavirus RNA-Dependent RNA Polymerase/immunology , Humans , Mutation , RNA, Viral/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/analysis , Spike Glycoprotein, Coronavirus/immunology , Temperature
15.
Sci Rep ; 11(1): 7430, 2021 04 01.
Article in English | MEDLINE | ID: covidwho-1162021

ABSTRACT

Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.


Subject(s)
Chiroptera/virology , Genome, Viral , Virome/genetics , Animals , Chlorocebus aethiops , Germany , High-Throughput Nucleotide Sequencing , Nairovirus/classification , Nairovirus/genetics , Orbivirus/classification , Orbivirus/genetics , Phylogeny , Polymerase Chain Reaction , Rotavirus/classification , Rotavirus/genetics , Vero Cells , Viruses/classification , Viruses/genetics
16.
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
17.
Sci Rep ; 11(1): 11545, 2021 06 02.
Article in English | MEDLINE | ID: covidwho-1253983

ABSTRACT

The Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the rapid depletion of public health resources in most countries. RT-PCR is Covid-19's reference diagnostic method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach and represented by co-occurrence matrices. This technique eliminates multiple sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. When comparing SARS-CoV-2 with virus families with similar symptoms, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP classifier and 30% overlap. When SARS-CoV-2 is compared to other coronaviruses and healthy human DNA sequences, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify DNA sequences for SARS-CoV-2 with greater specificity and sensitivity.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , Computational Biology/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , DNA, Viral , Humans , Machine Learning , Sensitivity and Specificity , Support Vector Machine , Viruses/genetics
18.
Pediatr Cardiol ; 42(7): 1526-1530, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1227834

ABSTRACT

Viral bronchiolitis is a relative contraindication to elective pediatric cardiac surgery. Nasopharyngeal swab utilizing polymerase chain reaction (PCR) screening for viruses known to cause bronchiolitis are commonly available. The objective of this study was to evaluate clinical outcomes in patients with nasopharyngeal viral PCR positive findings at the time of cardiac surgery. Retrospective review from January 2013 to May 2019 for patients with virus detected by PCR on nasopharyngeal swabs at the time of cardiac surgery. Single ventricle and two ventricle patients were compared to control group of age and procedure matched patients viral negative at the time of surgery. Outcome measures included OR extubation, reintubation, hospital length of stay, and mortality. For two ventricle patients (n = 81; control group = 165), there was no statistical difference in any outcome variable (OR extubation 74% vs 72%; p = 0.9; reintubation 9% vs 11% vs; p = 0.7; hospital length of stay 5 days (1-46) vs 4 days (2-131); p = 0.4; mortality 2 vs 1; p = 0.3). For single ventricle patients, there was no statistical difference in any outcome variable (OR extubation 81% vs 76%; p = 0.6; reintubation 14% vs 21% vs; p = 0.5; hospital length of stay 9.5 days (3-116) vs 15 days (2-241); p = 0.1; mortality 0 vs 3; (p = 0.6)). PCR is a sensitive test that fails to predict which patients will proceed to have a clinically significant infection. Viral bronchiolitis remains a relative risk factor for cardiac surgery; presence of detectable virus via nasopharyngeal swab with limited clinical symptoms may not be a contraindication to cardiac surgery.


Subject(s)
Cardiac Surgical Procedures , Airway Extubation , Cardiac Surgical Procedures/adverse effects , Child , Humans , Intubation, Intratracheal , Polymerase Chain Reaction , Retrospective Studies
19.
J Virol Methods ; 294: 114171, 2021 08.
Article in English | MEDLINE | ID: covidwho-1226315

ABSTRACT

Respiratory syncytial virus (RSV) is a common cause of acute respiratory disease worldwide, especially in young children. The World Health Organization (WHO) has initiated an RSV Surveillance Pilot program that aims to perform worldwide RSV surveillance, requiring the development of reliable and rapid molecular methods to detect and identify RSV. A duplex real-time RT-PCR assay developed for simultaneous detection of both A and B subtypes of RSV was included as part of this program. This duplex assay targeted a conserved region of the RSV polymerase gene and was validated for analytical sensitivity, specificity, reproducibility and clinical performance with a wide range of respiratory specimens. The assay was highly specific for RSV and did not react with non-RSV respiratory pathogens, including the SARS-CoV-2 virus.


Subject(s)
Molecular Diagnostic Techniques/methods , RNA, Viral/isolation & purification , Respiratory Syncytial Virus, Human/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , DNA Primers/genetics , Humans , Limit of Detection , Nasopharynx/virology , RNA-Dependent RNA Polymerase/genetics , Reproducibility of Results , Ribonuclease P/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
20.
Cureus ; 13(4): e14250, 2021 Apr 01.
Article in English | MEDLINE | ID: covidwho-1218713

ABSTRACT

Acute myocarditis is commonly caused by viral infections resulting from viruses such as adenovirus, enteroviruses, and, rarely, coronavirus. It presents with nonspecific symptoms like chest pain, dyspnea, palpitation, or arrhythmias and can progress to dilated cardiomyopathy or heart failure. Fulminant myocarditis is a potentially life-threatening form of the condition and presents as acute, severe heart failure with cardiogenic shock. In this report, we discuss a case of a 41-year-old female who presented with cough and chest pain of two days' duration. The patient had a new-onset atrial flutter. Her chest auscultation revealed bilateral crackles. Laboratory workup revealed elevated troponin levels, and the patient tested positive for coronavirus disease 2019 (COVID-19) by nasopharyngeal swab polymerase chain reaction (PCR). Transthoracic echocardiogram revealed a low left ventricular (LV) ejection fraction of 35-40% compared to 55% one year prior, as well as a granular appearance of LV myocardium. The patient's condition subsequently improved clinically and she was discharged home. Due to cardiac involvement and characteristic myocardial appearance on the echocardiogram, cardiac magnetic resonance (CMR) imaging was performed for further evaluation about two months from the date of admission. CMR showed extensive myocardial inflammation with a typical pattern of sub-epicardial and mid-wall delayed enhancement, confirming the diagnosis of myocarditis. This case highlights myocarditis as a potential complication of COVID-19 that requires early diagnosis and proper management to improve patients' quality of life. Additionally, we highlight the features of myocarditis on CMR in the acute phase and two months after clinical recovery.

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