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1.
urol. colomb. (Bogotá. En línea) ; 31(4): 170-176, 2022. ilus
Article in Spanish | WHO COVID, LILACS (Americas) | ID: covidwho-2186455

ABSTRACT

Objetivo Describir la tasa de mortalidad de infección por coronavirus de tipo 2 causante del síndrome respiratorio agudo severo (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, en inglés) y los factores de riesgo asociados a la severidad de la enfermedad en pacientes con trasplante renal de un centro del nordeste colombiano. Materiales y Métodos Estudio descriptivo de una cohorte de pacientes en seguimiento postrasplante renal, en el que se hizo una búsqueda retrospectiva de los que presentaron infección por SARS-CoV-2 entre marzo del 2020 y mayo del 2021. Para el análisis, se incluyeron los pacientes con infección confirmada mediante pruebas de reacción en cadena de la polimerasa (polymerase chain reaction, PCR, en inglés), de antígenos, o de anticuerpos. Se realizó un análisis descriptivo de las variables sociodemográficas y clínicas, y un análisis bivariado de los posibles factores asociados con el riesgo de mortalidad. Resultados Con un total de 307 individuos en seguimiento, se encontró una prevalencia del 14,3% (n = 44) de infección por enfermedad por coronavirus 2019 (coronavirus disease 2019, COVID-19, en inglés). La media de edad fue de 56 años, con predominio del género masculino. El esquema de inmunosupresión más frecuente fue micofenolato­tacrolimus­prednisona. Entre los pacientes infectados, la mortalidad fue del 34,1% (15/44), lo que representa el 4,8% de toda la población a estudio. Maás de la mitad de los pacientes requirieron hemodiálisis, y en el 86,7% fue necesario hacer ajustes en el esquema de inmunosupresión. Conclusión La prevalencia de infección por SARS-CoV-2 en nuestro grupo de trasplantes fue similar a la reportada por otros grupos de trasplante del país, y mayor a la de la población no trasplantada. El valor de creatinina previo a la infección, la edad y las comorbilidades se asociaron con un mayor riesgo de mortalidad.


Objective To describe the mortality related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the risk factors associated with disease severity in patients submitted to a kidney transplant from a center in northeastern Colombia. Materials and Methods The present is a descriptive study of a cohort of patients in follow-up care after kidney transplant, with a retrospective search for those who presented SARS-CoV-2 infection between March 2020 and May 2021. Patients with confirmed infection by polymerase chain reaction (PCR), antigens or antibodies tests were included for analysis. We performed a descriptive analysis of the sociodemographic and clinical variables as well as a bivariate analysis to evaluate the possible factors associated with the risk of mortality. Results With a total of 307 individuals in follow-up care, a prevalence of 14.3% (n = 44) of coronavirus disease 2019 (COVID-19) infection was found. The mean age of the sample was of 56 years, with a male predominance. The most frequent immunosuppression regimen was mycophenolate-tacrolimus-prednisone. Among the infected patients, the mortality rate was of 34.1% (15/44), representing 4.8% of the entire study population. More than half of the patients required hemodialysis, and 86.7% required adjustments to the immunosuppression regimen. Conclusion The prevalence of SARS-CoV-2 infection in our transplant group was similar to that reported by other transplant groups in the country and higher than among the non-transplanted population. The preinfection creatinine value, age, and comorbidities were associated with a higher risk of mortality.


Subject(s)
Humans , Male , Female , Middle Aged , Renal Dialysis , Kidney Transplantation , Coronavirus , Severe Acute Respiratory Syndrome , SARS-CoV-2 , COVID-19 , Severity of Illness Index , Adaptation, Psychological , Polymerase Chain Reaction , Risk Factors , Immunosuppression Therapy , Antigens
2.
Parasitol Res ; 121(7): 1867-1885, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-2174153

ABSTRACT

Malaria control measures have been in use for years but have not completely curbed the spread of infection. Ultimately, global elimination is the goal. A major playmaker in the various approaches to reaching the goal is the issue of proper diagnosis. Various diagnostic techniques were adopted in different regions and geographical locations over the decades, and these have invariably produced diverse outcomes. In this review, we looked at the various approaches used in malaria diagnostics with a focus on methods favorably used during pre-elimination and elimination phases as well as in endemic regions. Microscopy, rapid diagnostic testing (RDT), loop-mediated isothermal amplification (LAMP), and polymerase chain reaction (PCR) are common methods applied depending on prevailing factors, each with its strengths and limitations. As the drive toward the elimination goal intensifies, the search for ideal, simple, fast, and reliable point-of-care diagnostic tools is needed more than ever before to be used in conjunction with a functional surveillance system supported by the ideal vaccine.


Subject(s)
Malaria, Falciparum , Malaria , Diagnostic Tests, Routine/methods , Goals , Humans , Malaria/diagnosis , Malaria/prevention & control , Malaria, Falciparum/epidemiology , Microscopy/methods , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Polymerase Chain Reaction/methods , Sensitivity and Specificity
3.
Klin Lab Diagn ; 67(11): 678-684, 2022 Nov 14.
Article in English | MEDLINE | ID: covidwho-2146786

ABSTRACT

The issues of laboratory diagnostics have been relevant since the first days of the SARS-CoV-2 pandemic and play a key role in the fight against the spread of a new coronavirus infection. A direct method for the etiological diagnosis of the causative agent of COVID-19 is the detection of SARS-CoV-2 RNA using the nucleic acid amplification method. In the context of a pandemic and the mass appeal of patients for medical care, the issues of ensuring the quality of ongoing molecular biological studies at all stages (preanalytical, analytical, postanalytical) become the most relevant. the results and timing of the study not only affect the diagnosis and treatment tactics of a particular patient, but are also the basis for the introduction of anti-epidemic measures, the adoption of organizational measures. The study is to summarize the experience in creating an effective and reliable system for managing the quality of molecular biological research in a pandemic using the example of a federal budgetary healthcare institution. The experience of the laboratory of a federal healthcare institution in the context of the COVID-19 pandemic was analyzed, errors were analyzed at the preanalytical, analytical and postanalytical stages of PCR studies with the identification of quality criteria, the impact on which significantly leads to quality improvement. The quality control system for PCR studies is based on the development of regulatory documents and instructions for the patient and laboratory staff, registration of all documents in a single information system with access to information from all structural divisions, with the possibility of uploading data to the patient's personal account on the institution's website. Quality indicators of all stages of PCR studies and measures that significantly affect the quality of laboratory studies were identified; Measures have been identified to reduce the turnaround time of a PCR test: distribution of biomaterial flows, optimization of operators' work, purchase of additional equipment, a patient feedback system, and an infection control information system. The obtained results make it possible to create a reliable quality control system, minimize the risk of obtaining erroneous research results, optimizing the work of the clinical diagnostic laboratory and increasing its productivity.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , Pandemics , RNA, Viral , SARS-CoV-2/genetics , Polymerase Chain Reaction
4.
Clin Lab Med ; 42(2): 283-298, 2022 06.
Article in English | MEDLINE | ID: covidwho-2130436

ABSTRACT

Deployment of molecular testing for SARS-CoV-2 in resource-limited settings is challenging. Scale-up of molecular had to be conducted with a laboratory system strengthening approach that emphasize laboratory integration. National reference laboratories play a central role. In Malawi the molecular testing was underpinned by existing pathogen control programs for human immunodeficiency virus and tuberculosis that use Abbott and GeneXpert machines and reagents. Despite this, the impact on these programs was well managed. Antigen testing increased access to testing. Pooled testing and direct-to-polymerase chain reaction methods have the potential to save costs and further increase access to molecular tests.


Subject(s)
COVID-19 , HIV Infections , COVID-19/diagnosis , Humans , Molecular Diagnostic Techniques , Polymerase Chain Reaction , SARS-CoV-2/genetics
5.
Molecules ; 27(20)2022 Oct 18.
Article in English | MEDLINE | ID: covidwho-2110187

ABSTRACT

Early and rapid diagnosis of pathogens is important for the prevention and control of epidemic disease. The polymerase chain reaction (PCR) technique requires expensive instrument control, a special test site, complex solution treatment steps and professional operation, which can limit its application in practice. The pathogen detection method based on the clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated protein (CRISPR/Cas) system is characterized by strong specificity, high sensitivity and convenience for detection, which is more suitable for practical applications. This article first reviews the CRISPR/Cas system, and then introduces the application of the two types of systems represented by Type II (cas9), Type V (cas12a, cas12b, cas14a) and Type VI (cas13a) in pathogen detection. Finally, challenges and prospects are proposed.


Subject(s)
CRISPR-Associated Proteins , CRISPR-Cas Systems , CRISPR-Cas Systems/genetics , Gene Editing/methods , Polymerase Chain Reaction , CRISPR-Associated Proteins/genetics
6.
Viruses ; 14(11)2022 Nov 21.
Article in English | MEDLINE | ID: covidwho-2123865

ABSTRACT

A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation PCR-based protocols were not always specific, and consequently, determination of a high number of informative sites was needed for accurate lineage identification. A detailed in silico analysis of SARS-CoV-2 sequences retrieved from GISAID database revealed the S gene 921 bp-fragment, positions 22784-23705 of SARS-CoV-2 reference genome, as the most informative fragment (30 variable sites) to determine relevant SARS-CoV-2 variants. Consequently, a method consisting of the PCR-amplification of this fragment, followed by Sanger's sequencing and a "single-click" informatic program based on a reference database, was developed and validated. PCR-fragments obtained from clinical SARS-CoV-2 samples were compared with homologous variant-sequences and the resulting phylogenetic tree allowed the identification of Alpha, Delta, Omicron, Beta, Gamma, and other variants. The data analysis procedure was automatized and simplified to the point that it did not require specific technical skills. The method is faster and cheaper than current whole-genome sequencing methods; it is available worldwide, and it may help to enhance efficient surveillance in the fight against the COVID-19 pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Phylogeny , Genome, Viral , COVID-19/diagnosis , COVID-19/epidemiology , Pandemics , Polymerase Chain Reaction
7.
Front Immunol ; 13: 1022750, 2022.
Article in English | MEDLINE | ID: covidwho-2119842

ABSTRACT

Immune responses affiliated with COVID-19 severity have been characterized and associated with deleterious outcomes. These approaches were mainly based on research tools not usable in routine clinical practice at the bedside. We observed that a multiplex transcriptomic panel prototype termed Immune Profiling Panel (IPP) could capture the dysregulation of immune responses of ICU COVID-19 patients at admission. Nine transcripts were associated with mortality in univariate analysis and this 9-mRNA signature remained significantly associated with mortality in a multivariate analysis that included age, SOFA and Charlson scores. Using a machine learning model with these 9 mRNA, we could predict the 28-day survival status with an Area Under the Receiver Operating Curve (AUROC) of 0.764. Interestingly, adding patients' age to the model resulted in increased performance to predict the 28-day mortality (AUROC reaching 0.839). This prototype IPP demonstrated that such a tool, upon clinical/analytical validation and clearance by regulatory agencies could be used in clinical routine settings to quickly identify patients with higher risk of death requiring thus early aggressive intensive care.


Subject(s)
COVID-19 , Critical Illness , Humans , RNA, Messenger , Hospitalization , Polymerase Chain Reaction
8.
Travel Med Infect Dis ; 50: 102459, 2022.
Article in English | MEDLINE | ID: covidwho-2118175

ABSTRACT

Monkeypox is an emerging zoonotic disease caused by monkeypox virus which is a DNA virus. The virus is transmitted to humans as a result of close contact with infected animals, infected humans or contaminated inanimate objects. The disease has a incubation period usually 7-14 days and it causes fever, headache, fatigue, myalgia, widespread body aches, swelling in lymph nodes and skin lesions. It may be difficult to distinguish monkeypox on the basis of clinical presentation alone, especially for cases with an atypical appearance, because of the various conditions that cause skin rashes. Testing should be offered to anyone who falls under the suspected case definition for monkeypox infection. Suitable samples are surface lesion and/or skin materials such as exudates swabs and crusts. Laboratory confirmation of specimens from suspected case is done using nucleic acid amplification testing, such as real-time or conventional polymerase chain reaction. Confirmation of MPXV infection should consider clinical and epidemiological information. Positive detection using an OPXV PCR assay followed by confirmation of MPXV via PCR and/or sequencing, or positive detection using MPXV PCR assay in suspected cases indicates confirmation of MPXV infection. Genetic sequence data (GSD) provide information on the origin and epidemic and characteristics of cases. There is a need to develop a more global and effective laboratory network for this emerging zoonosis, as well as to strengthen laboratory capacity, and international specimens referral capacities.


Subject(s)
Monkeypox virus , Monkeypox , Animals , Humans , Monkeypox virus/genetics , Monkeypox/diagnosis , Monkeypox/epidemiology , Monkeypox/pathology , Polymerase Chain Reaction , Nucleic Acid Amplification Techniques
9.
Sci Rep ; 12(1): 18651, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2106457

ABSTRACT

Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/genetics , COVID-19 Testing , Polymerase Chain Reaction , Mutation , Sensitivity and Specificity
10.
Anal Methods ; 14(45): 4625-4642, 2022 Nov 24.
Article in English | MEDLINE | ID: covidwho-2106523

ABSTRACT

The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Polymerase Chain Reaction , Nucleotides
11.
Front Public Health ; 10: 994712, 2022.
Article in English | MEDLINE | ID: covidwho-2099270

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic can be effectively controlled by rapid and accurate identification of SARS-CoV-2-infected cases through large-scale screening. Hypercube pooling polymerase chain reaction (PCR) is frequently used as a pooling technique because of its high speed and efficiency. We attempted to implement the hypercube pooling strategy and found it had a large quantization effect. This raised two questions: is hypercube pooling with edge = 3 actually the optimal strategy? If not, what is the best edge and dimension? We used a C++ program to calculate the expected number of PCR tests per patient for different values of prevalence, edge, and dimension. The results showed that every edge had a best performance range. Then, using C++ again, we created a program to calculate the optimal edge and dimension required for pooling samples when entering prevalence into our program. Our program will be provided as freeware in the hope that it can help governments fight the SARS-CoV-2 pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19 Testing , COVID-19/diagnosis , Pandemics , Polymerase Chain Reaction
12.
Respir Res ; 23(1): 297, 2022 Oct 31.
Article in English | MEDLINE | ID: covidwho-2098346

ABSTRACT

BACKGROUND: Routine follow-up of patients hospitalised with COVID-19 is recommended, however due to the ongoing high number of infections this is not without significant health resource and economic burden. In a previous study we investigated the prevalence of, and risk factors for, persistent chest radiograph (CXR) abnormalities post-hospitalisation with COVID-19 and identified a 5-point composite score that strongly predicted risk of persistent CXR abnormality at 12-weeks. Here we sought to validate and refine our findings in an independent cohort of patients. METHODOLOGY: A single-centre prospective study of consecutive patients attending a virtual post-hospitalisation COVID-19 clinic and CXR as part of their standard clinical care between 2nd March - 22nd June 2021. Inpatient and follow-up CXRs were scored by the assessing clinician for extent of pulmonary infiltrates (0-4 in each lung) with complete resolution defined as a follow-up score of zero. RESULTS: 182 consecutive patients were identified of which 31% had persistent CXR abnormality at 12-weeks. Patients with persistent CXR abnormality were significantly older (p < 0.001), had a longer hospital length of stay (p = 0.005), and had a higher incidence of both level 2 or 3 facility admission (level 2/3 care) (p = 0.003) and ever-smoking history (p = 0.038). Testing our composite score in the present cohort we found it predicted persistent CXR abnormality with reasonable accuracy (area under the receiver operator curve [AUROC 0.64]). Refining this score replacing obesity with Age ≥ 50 years, we identify the SHADE-750 score (1-point each for; Smoking history, Higher-level care (level 2/3 admission), Age ≥ 50 years, Duration of admission ≥ 15 days and Enzyme-lactate dehydrogenase (LDH ≥ 750U/L), that accurately predicted risk of persistent CXR abnormality, both in the present cohort (AUROC 0.73) and when retrospectively applied to our 1st cohort (AUROC 0.79). Applied to both cohorts combined (n = 213) it again performed strongly (AUROC 0.75) with all patients with a score of zero (n = 18) having complete CXR resolution at 12-weeks. CONCLUSIONS: In two independent cohorts of patients hospitalised with COVID-19, we identify a 5-point score which accurately predicts patients at risk of persistent CXR abnormality at 12-weeks. This tool could be used by clinicians to identify patients in which radiological follow-up may not be required.


Subject(s)
COVID-19 , Humans , Middle Aged , SARS-CoV-2 , Retrospective Studies , Prospective Studies , Radiography, Thoracic , Hospitalization , L-Lactate Dehydrogenase , Risk Factors , Polymerase Chain Reaction
14.
Virol J ; 19(1): 168, 2022 10 27.
Article in English | MEDLINE | ID: covidwho-2089213

ABSTRACT

BACKGROUND: SARS-CoV-2 variant tracking is key to the genomic surveillance of the COVID-19 pandemic. While next-generation sequencing (NGS) is commonly used for variant determination, it is expensive and time-consuming. Variant-specific PCR (vsPCR) is a faster, cheaper method that detects specific mutations that are considered variant-defining. These tests usually rely on specific amplification when a mutation is present or a specific melting temperature peak after amplification. CASE PRESENTATION: A discrepant result between vsPCR and NGS was found in seventeen SARS-CoV-2 samples from Galicia, Spain. A cluster of BA.1 Omicron SARS-CoV-2 variant showed a BA.2-like melting temperature pattern due to a point mutation (C21772T) downstream the deletion of the spike amino acids 69/70. As the 69/70 deletion is widely used for differentiation between BA.1 and BA.2 by vsPCR, C21772T can cause BA.1 samples to be misinterpreted as BA.2. Over a thousand BA.1 sequences in the EpiCoV database contain this mutation. CONCLUSIONS: To our knowledge, this is the first case of a point mutation causing a vsPCR algorithm to misclassify BA.1 samples as BA.2. This is an example of how mutations in the probe target area of vsPCR tests based on melting curve analysis can lead to variant misclassification. NGS confirmation of vsPCR results is relevant for the accuracy of the epidemiological surveillance. In order to overcome the possible impact of novel mutations, diagnostic tools must be constantly updated.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Point Mutation , Pandemics , COVID-19/diagnosis , Polymerase Chain Reaction , Mutation
15.
Medicine (Baltimore) ; 101(42): e31278, 2022 Oct 21.
Article in English | MEDLINE | ID: covidwho-2087899

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is a major challenge for global healthcare systems. Early and safe triage in the emergency department (ED) is crucial for proper therapy. However, differential diagnosis remains challenging. Rapid antigen testing (RAT) may help to improve early triage and patient safety. We performed a retrospective study of 234 consecutive patients with suspected COVID-19 who presented to our ED in November 2020. All underwent SARS-CoV-2-nasopharyngeal swab testing using both RAT and reverse transcription polymerase chain reaction (RT-PCR). The inpatient treatment was established according to an empirically developed triage algorithm. The accuracy of the suggested algorithm was analyzed based on the rate of outpatients returning within 7 days and inpatients staying for less than 48 hours. COVID-19 inpatients and outpatients were compared for symptoms, vital signs, and C-reactive protein levels. Of the 221 included patients with suspected COVID-19 infection, the diagnosis could be confirmed in 120 patients (54.3%) by a positive RT-PCR result, whereas only 72% of those had a positive antigen test. Of the 56 COVID-19 outpatients, three returned within 7 days with the need for hospital treatment due to clinical deterioration. Among the 64 COVID-19 inpatients, 4 were discharged within 48 hours, whereas 60 stayed longer (mean duration 10.2 days). The suggested triage algorithm was safe and efficient in the first 234 consecutive patients. RAT can confirm a diagnosis in 72% of PCR proven COVID-19 patients and allows early cohort isolation as an important way to save hospital capacity.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2/genetics , Triage , Retrospective Studies , Case-Control Studies , C-Reactive Protein , Emergency Service, Hospital , Algorithms , Polymerase Chain Reaction
16.
Exp Gerontol ; 170: 111998, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2086199

ABSTRACT

PURPOSE: While the definitive diagnosis of COVID-19 relies on PCR confirmation of the virus, the sensitivity of this technique is limited. The clinicians had to go on with the clinical diagnosis of COVID-19 in selected cases. We aimed to compare PCR-positive and PCR-negative patients diagnosed as COVID-19 with a specific focus on older adults. METHODS: We studied 601 hospitalized adults. The demographics, co-morbidities, triage clinical, laboratory characteristics, and outcomes were noted. Differences between the PCR (+) and (-) cases were analyzed. An additional specific analysis focusing on older adults (≥65 years) (n = 184) was performed. RESULTS: The PCR confirmation was present in 359 (59.7 %). There was not any difference in terms of age, sex, travel/contact history, hospitalization duration, ICU need, the time between first symptom/hospitalization to ICU need, ICU days, or survival between PCR-positive and negative cases in the total study group and older adults subgroup. The only symptoms that were different in prevalence between PCR-confirmed and unconfirmed cases were fever (73.3 % vs. 64 %, p = 0.02) and fatigue/myalgia (91.1 % vs. 79.3 %, p = 0.001). Bilateral diffuse pneumonia was also more prevalent in PCR-confirmed cases (20 % vs. 13.3 %, p = 0.03). In older adults, the PCR (-) cases had more prevalent dyspnea (72.2 % vs. 51.4 %, p = 0.004), less prevalent fatigue/myalgia (70.9 % vs. 88.6 %, p = 0.002). CONCLUSION: The PCR (+) and (-) cases displayed very similar disease phenotypes, courses, and outcomes with few differences between each other. The presence of some worse laboratory findings may indicate a worse immune protective response in PCR (-) cases.


Subject(s)
COVID-19 , Pneumonia , Humans , COVID-19/diagnosis , SARS-CoV-2 , Myalgia , Hospitalization , Polymerase Chain Reaction , Outcome Assessment, Health Care , Fatigue
17.
J Occup Environ Med ; 64(9): e575-e578, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-2077945

ABSTRACT

OBJECTIVE: The aim of this study was to determine whether mid-turbinate specimens reliably detect active infection in asymptomatic adults undergoing regular COVID-19 PCR testing. METHODS: Qualitative agreement between 2481 paired nasopharyngeal and mid-turbinate PCR results was assessed. Mean cycle threshold values for each positive result were evaluated as an indicator of active infection. RESULTS: Overall agreement between nasopharyngeal and mid-turbinate tests was 98.4%. Positive percent agreement was 37.2%, and negative percent agreement was ~100%. Test pairs with lower cycle thresholds (≤30 and ≤25) reached 67% and 100% positive percent agreement, respectively. CONCLUSIONS: SARS-CoV-2 infections with high viral loads were detected regardless of specimen type. Mid-turbinate swabs reduced staff discomfort and may decrease repeated positive test results weeks or months after initial infection. Discordant pairs generally had high cycle threshold values (>30) indicating low viral load and little risk of transmitting COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , COVID-19/diagnosis , COVID-19 Testing , Humans , Nasopharynx , Polymerase Chain Reaction , Sensitivity and Specificity , Turbinates
18.
Sensors (Basel) ; 22(19)2022 Sep 23.
Article in English | MEDLINE | ID: covidwho-2066346

ABSTRACT

Thermal inkjet printing can generate more than 300,000 droplets of picoliter scale within one second stably, and the image analysis workflow is used to quantify the positive and negative values of the droplets. In this paper, the SimpleBlobDetector detection algorithm is used to identify and localize droplets with a volume of 24 pL in bright field images and suppress bright spots and scratches when performing droplet location identification. The polynomial surface fitting of the pixel grayscale value of the fluorescence channel image can effectively compensate and correct the image vignetting caused by the optical path, and the compensated fluorescence image can accurately classify positive and negative droplets by the k-means clustering algorithm. 20 µL of the sample solution in the result reading chip can produce more than 100,000 effective droplets. The effective droplet identification correct rate of 20 images of random statistical samples can reach more than 99% and the classification accuracy of positive and negative droplets can reach more than 98% on average. This paper overcomes the problem of effectively classifying positive and negative droplets caused by the poor image quality of photographed picolitre ddPCR droplets caused by optical hardware limitations.


Subject(s)
Algorithms , Image Processing, Computer-Assisted , Cluster Analysis , Polymerase Chain Reaction , Technology
19.
Nat Commun ; 13(1): 5822, 2022 10 12.
Article in English | MEDLINE | ID: covidwho-2062206

ABSTRACT

Disease characterization of Post-Acute Sequelae of SARS-CoV-2 (PASC) does not account for pre-existing conditions and time course of incidence. We utilized longitudinal data and matching to a COVID PCR-negative population to discriminate PASC conditions over time within our patient population during 2020. Clinical Classification Software was used to identify PASC condition groupings. Conditions were specified acute and persistent (occurring 0-30 days post COVID PCR and persisted 30-120 days post-test) or late (occurring initially 30-120 days post-test). We matched 3:1 COVID PCR-negative COVIDPCR-positive by age, sex, testing month and service area, controlling for pre-existing conditions up to four years prior; 28,118 PCR-positive to 70,293 PCR-negative patients resulted. We estimated PASC risk from the matched cohort. Risk of any PASC condition was 12% greater for PCR-positive patients in the late period with a significantly higher risk of anosmia, cardiac dysrhythmia, diabetes, genitourinary disorders, malaise, and nonspecific chest pain. Our findings contribute to a more refined PASC definition which can enhance clinical care.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/complications , Cohort Studies , Disease Progression , Humans , Polymerase Chain Reaction
20.
Transbound Emerg Dis ; 69(5): e3045-e3059, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2053039

ABSTRACT

Isolation of porcine reproductive and respiratory syndrome virus (PRRSV) in cell culture is a primary means of obtaining virus isolates for autogenous vaccine production and other applications. However, it has not been well characterized whether cell culture isolate and the virus in clinical sample are equivalent. This study compared PRRSV ORF5 sequences from 1024 clinical samples (995 PRRSV-2, 26 PRRSV-1, and three PRRSV-1 and PRRSV-2 PCR-positive) and their isolates in MARC-145 and/or ZMAC cells. For three PRRSV-1 and PRRSV-2 PCR-positive clinical samples, both PRRSV-1 and PRRSV-2 were isolated in ZMAC cells, whereas either PRRSV-1 or PRRSV-2, but not both, was isolated in MARC-145 cells, with isolate sequences matching the respective viruses in clinical samples. Twenty-six PRRSV-1 and most of 995 PRRSV-2 PCR-positive clinical samples had matching viral ORF5 sequences with their cell culture isolates. However, 14 out of 995 PRRSV-2 cases (1.4%) had nonmatching viral sequences between clinical samples and MARC-145 isolates, although viral sequences from clinical samples and ZMAC isolates matched. This is concerning because, if the MARC-145 isolate is directly used for autogenous vaccine production without sequencing confirmation against the virus in the clinical sample, it is possible that the produced autogenous vaccine does not include the desired wild-type virus strain found on the farm and instead contains vaccine-like virus. Vaccine-specific PCR and next-generation sequencing performed on six selected cases indicated presence of ≥2 PRRSV-2 strains (mixed infection) in such clinical samples. In summary, PRRSV ORF5 sequences from clinical samples and cell culture isolates matched each other for majority of the cases. However, PRRSV sequences between clinical sample and MARC-145 cell culture isolate could occasionally be different when the clinical sample contains ≥2 PRRSV-2 strains. Characterizing PRRSV sequences from clinical samples and cell culture isolates should be conducted before using isolates for producing autogenous vaccines or other applications.


Subject(s)
Autovaccines , Porcine Reproductive and Respiratory Syndrome , Porcine respiratory and reproductive syndrome virus , Swine Diseases , Animals , Cell Culture Techniques/veterinary , Phylogeny , Polymerase Chain Reaction/veterinary , Porcine respiratory and reproductive syndrome virus/genetics , Swine
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