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1.
Crit Care ; 26(1): 10, 2022 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-34983614

RESUMO

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.


Assuntos
COVID-19 , SARS-CoV-2 , Adulto , COVID-19/terapia , COVID-19/virologia , Teste de Ácido Nucleico para COVID-19 , Estado Terminal , Humanos , Unidades de Terapia Intensiva , Nasofaringe/virologia , Estudos Prospectivos , SARS-CoV-2/isolamento & purificação
2.
Int J Cancer ; 150(3): 431-439, 2022 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-34610144

RESUMO

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.


Assuntos
COVID-19/diagnóstico , Programas Obrigatórios , Neoplasias/complicações , Quarentena , SARS-CoV-2/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/epidemiologia , COVID-19/prevenção & controle , COVID-19/transmissão , Teste de Ácido Nucleico para COVID-19 , Feminino , Humanos , Itália/epidemiologia , Masculino , Pessoa de Meia-Idade , Neoplasias/epidemiologia , Neoplasias/virologia , Pandemias , Estudos Retrospectivos , SARS-CoV-2/genética , Viagem
4.
J Med Virol ; 94(1): 240-245, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34460115

RESUMO

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.


Assuntos
Teste de Ácido Nucleico para COVID-19 , COVID-19/diagnóstico , COVID-19/epidemiologia , Adolescente , Adulto , Infecções Assintomáticas/epidemiologia , COVID-19/virologia , Criança , Pré-Escolar , Estudos Transversais , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , SARS-CoV-2/fisiologia , Carga Viral , Adulto Jovem
5.
J Med Virol ; 94(1): 413-416, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34515998

RESUMO

In December 2020, Italy experienced the first case of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) B.1.1.7 lineage. In January 2021, we identified 21 cases of this variant in Corzano, defining the first outbreak of SARS-CoV-2 B.1.1.7 lineage in Italy. The high transmissibility of the B.1.1.7 variant represented an important benefit for the virus, which became rapidly dominant on the territory. Containment measures induced the epidemic curve onto a decreasing trajectory underlining the importance of appropriate control and surveillance for restraint of virus spread. Highlights The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage occurred in Lombardy in January 2021. The outbreak originated by a single introduction of the B.1.1.7 lineage. The genomic sequencing revealed, for the first time, the presence of the V551F mutation in the B.1.1.7 lineage in Italy. Surveillance, prompt sequencing and tracing efforts were fundamental to identify and to quickly contain the outbreak.


Assuntos
Teste de Ácido Nucleico para COVID-19 , COVID-19/epidemiologia , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Adolescente , Adulto , COVID-19/transmissão , Criança , Pré-Escolar , Surtos de Doenças/estatística & dados numéricos , Feminino , Genoma Viral/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Controle de Infecções/métodos , Itália/epidemiologia , Masculino , Pessoa de Meia-Idade , Filogenia , Análise de Sequência de RNA , Sequenciamento Completo do Genoma , Adulto Jovem
6.
Porto Alegre; CEVS/RS; dez. 2021. 1-27 p. ilus., graf., tab., mapas.
Não convencional em Português | Coleciona SUS, CONASS, SES-RS | ID: biblio-1349442

RESUMO

Neste boletim são apresentados: situação mundial, ocorrência de hospitalizações confirmadas para sars-cov-2, perfil das pessoas, distribuição espacial, Síndrome Inflamatória Multissistêmica Pediátrica (SIM-P), povos indígenas, descrição de surtos, trabalhadores da saúde, Vigilância sentinela de síndrome gripal e tabelas de descrição do surto. (AU)


Assuntos
Humanos , Masculino , Feminino , Gravidez , Recém-Nascido , Lactente , Pré-Escolar , Criança , Adolescente , Adulto , Pessoa de Meia-Idade , Idoso , Idoso de 80 Anos ou mais , Perfil de Saúde , Mortalidade Hospitalar/etnologia , Pessoal de Saúde , Vigilância de Evento Sentinela , Grupos Populacionais/estatística & dados numéricos , Saúde de Populações Indígenas/estatística & dados numéricos , Teste de Ácido Nucleico para COVID-19 , COVID-19/epidemiologia , Hospitalização/estatística & dados numéricos , Saúde da Criança , Surtos de Doenças , Infecções por Coronavirus/mortalidade , Saúde do Adolescente , COVID-19/complicações
7.
Viruses ; 13(12)2021 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-34960655

RESUMO

As SARS-CoV-2 continues to spread among human populations, genetic changes occur and accumulate in the circulating virus. Some of these genetic changes have caused amino acid mutations, including deletions, which may have a potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics. Considerable efforts have been made to categorize the amino acid mutations of the angiotensin-converting enzyme 2 (ACE2) receptor binding domain (RBD) of the spike (S) protein, along with certain mutations in other regions within the S protein as specific variants, in an attempt to study the relationship between these mutations and the biological behavior of the virus. However, the currently used whole genome sequencing surveillance technologies can test only a small fraction of the positive specimens with high viral loads and often generate uncertainties in nucleic acid sequencing that needs additional verification for precision determination of mutations. This article introduces a generic protocol to routinely sequence a 437-bp nested RT-PCR cDNA amplicon of the ACE2 RBD and a 490-bp nested RT-PCR cDNA amplicon of the N-terminal domain (NTD) of the S gene for detection of the amino acid mutations needed for accurate determination of all variants of concern and variants of interest according to the definitions published by the U.S. Centers for Disease Control and Prevention. This protocol was able to amplify both nucleic acid targets into cDNA amplicons to be used as templates for Sanger sequencing on all 16 clinical specimens that were positive for SARS-CoV-2.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , Testes Diagnósticos de Rotina/métodos , SARS-CoV-2/genética , Sítios de Ligação/genética , COVID-19/diagnóstico , COVID-19/virologia , Humanos , Mutação , Domínios Proteicos/genética , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2/isolamento & purificação , Análise de Sequência de DNA , Glicoproteína da Espícula de Coronavírus/genética
8.
Viruses ; 13(12)2021 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-34960682

RESUMO

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.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Serviço Hospitalar de Emergência , Testes Imediatos , SARS-CoV-2/isolamento & purificação , COVID-19/epidemiologia , Croácia/epidemiologia , Humanos , RNA Viral/genética , Reprodutibilidade dos Testes , SARS-CoV-2/genética , Sensibilidade e Especificidade
9.
Viruses ; 13(12)2021 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-34960743

RESUMO

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.


Assuntos
Teste de Ácido Nucleico para COVID-19 , COVID-19/diagnóstico , Proteínas do Nucleocapsídeo de Coronavírus/genética , SARS-CoV-2/isolamento & purificação , Brasil/epidemiologia , COVID-19/epidemiologia , RNA-Polimerase RNA-Dependente de Coronavírus/genética , Primers do DNA , Reações Falso-Negativas , Genoma Viral/genética , Humanos , Mutação , Fosfoproteínas/genética , RNA Viral/genética , SARS-CoV-2/genética
10.
Medicine (Baltimore) ; 100(52): e28470, 2021 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-34967391

RESUMO

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.


Assuntos
Anticorpos Monoclonais Humanizados/uso terapêutico , Anticorpos Monoclonais/uso terapêutico , Antineoplásicos Imunológicos/uso terapêutico , COVID-19/tratamento farmacológico , Pneumonia/epidemiologia , Rituximab/uso terapêutico , Adulto , Idoso , COVID-19/diagnóstico , COVID-19/terapia , Teste de Ácido Nucleico para COVID-19 , Feminino , Humanos , Imunização Passiva , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , Recidiva , SARS-CoV-2 , Resultado do Tratamento
11.
Sci Rep ; 11(1): 24234, 2021 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-34930933

RESUMO

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.


Assuntos
Técnicas de Diagnóstico Molecular/métodos , Técnicas de Amplificação de Ácido Nucleico/métodos , RNA Viral/metabolismo , SARS-CoV-2/isolamento & purificação , COVID-19/diagnóstico , COVID-19/virologia , Teste de Ácido Nucleico para COVID-19/métodos , RNA-Polimerase RNA-Dependente de Coronavírus/genética , Humanos , Limite de Detecção , Nasofaringe/virologia , Proteínas do Nucleocapsídeo/genética , Sistemas Automatizados de Assistência Junto ao Leito , RNA Viral/genética , SARS-CoV-2/genética , SARS-CoV-2/metabolismo , Proteínas da Matriz Viral/genética
12.
Sci Rep ; 11(1): 23963, 2021 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-34907208

RESUMO

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.


Assuntos
COVID-19/epidemiologia , Mortalidade/tendências , SARS-CoV-2/isolamento & purificação , COVID-19/mortalidade , Teste de Ácido Nucleico para COVID-19 , Análise de Elementos Finitos , Hospitalização/estatística & dados numéricos , Humanos , Unidades de Terapia Intensiva , SARS-CoV-2/genética , Suécia/epidemiologia , Fatores de Tempo
13.
Ann Clin Lab Sci ; 51(6): 741-749, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34921026

RESUMO

OBJECTIVE: The ongoing COVID-19 pandemic caused by SARS-CoV-2 has challenged diagnostic laboratories to re-examine traditional methods for collecting specimens and sample types used in molecular testing. Our goal was to demonstrate that saliva can be used for detecting SARS-CoV-2 and correlates well with established molecular methods using nasopharyngeal (NP) swabs. METHODS: We examined use of a saliva collection device in conjunction with a laboratory-developed real-time reverse transcription-polymerase chain reaction (LDPCR) method for detecting SARS-CoV-2 in a symptomatic population and compared results with 2 US Food and Drug Administration (FDA)-approved methods (emergency use authorization [EUA]) that use specimens from NP swabs. RESULTS: The sensitivity of LDPCR compared with the reference methods was 75.0% (21/28); specificity, 98.1% (104/106). When cycle threshold values were compared between paired specimens using the LDPCR and a EUA reverse transcription PCR method, both targeting the open-reading frame gene, the mean value for saliva was 4.66 cycles higher than for NP specimens. CONCLUSION: Use of self-collected saliva in conjunction with an LDPCR for SARS-CoV-2 compared favorably with 2 FDA EUA methods using NP swabs. The use of an alternative sample type and assay method will aid in expanding the availability of testing during the ongoing COVID-19 pandemic.


Assuntos
COVID-19/diagnóstico , SARS-CoV-2/genética , Manejo de Espécimes/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/genética , Teste de Ácido Nucleico para COVID-19/métodos , Confiabilidade dos Dados , Testes Diagnósticos de Rotina/métodos , Feminino , Humanos , Laboratórios , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/métodos , Ácidos Nucleicos/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , SARS-CoV-2/patogenicidade , Saliva/química
14.
S Afr Med J ; 111(10): 957-960, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-34949289

RESUMO

BACKGROUND: The onset of the COVID-19 pandemic in South Africa (SA) created numerous supply challenges. Demand for diagnostic testing overwhelmed the capacity to deliver. We describe the utility and outcomes of a mobile laboratory staffed by non-laboratory healthcare workers and established to perform polymerase chain reaction (PCR) testing for the rapid diagnosis of COVID-19 at a large hospital in SA. OBJECTIVES: To describe the performance of the mobile PCR COVID-19 laboratory. The secondary objective was to determine the prevalence of COVID-19 infections in the non-COVID intensive care unit (ICU). METHODS: This was a retrospective descriptive study of data from the newly established mobile COVID-19 PCR laboratory database and the non-COVID ICU database during the first peak of the COVID-19 pandemic (20 May - 8 August 2020) at a tertiary hospital in SA. RESULTS: The mobile laboratory received 1 113 emergency COVID-19 PCR test requests for patients with non-COVID clinical presentations. The median (interquartile range) turnaround time was 152 (123 - 184) minutes (n=36). Primary outcome (20 May - 19 June, n=315): The sensitivity and specificity were 95% and 97%, respectively, and the positive and negative predictive values 82.4% and 99.2%, respectively. Secondary outcomes (9 June - 8 August): The prevalence of COVID-19 infections among patients admitted to the multidisciplinary adult and paediatric non-COVID ICU was 2.4% (n=4/168). The mean (standard deviation) COVID-19 positive rate for the mobile laboratory during this period was 18.1% (6%). The prevalence of COVID-19 infections among medical staff in the non-COVID ICU was 3.1% (n=1/32). CONCLUSIONS: The establishment of a mobile PCR laboratory staffed by non-laboratory healthcare workers during the COVID-19 pandemic provided a rapid, accurate and clinically effective solution for emergency hospital admissions with non-COVID-19 presentations.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Hospitalização/estatística & dados numéricos , Unidades Móveis de Saúde , Adolescente , Adulto , COVID-19/epidemiologia , Criança , Estudos Transversais , Feminino , Humanos , Unidades de Terapia Intensiva/estatística & dados numéricos , Laboratórios , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase/métodos , Valor Preditivo dos Testes , Estudos Retrospectivos , Sensibilidade e Especificidade , África do Sul , Centros de Atenção Terciária , Fatores de Tempo , Adulto Jovem
15.
PLoS One ; 16(12): e0261230, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34919584

RESUMO

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.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Técnicas de Laboratório Clínico/métodos , Testes Diagnósticos de Rotina/métodos , Programas de Rastreamento/métodos , Pandemias/prevenção & controle , Programas de Triagem Diagnóstica , Humanos , Universidades
16.
Heart Surg Forum ; 24(6): E940-E946, 2021 Nov 12.
Artigo em Inglês | MEDLINE | ID: mdl-34962467

RESUMO

BACKGROUND: The aim of this study was to investigate the clinical outcomes of cardiac surgery in patients who were incidentally diagnosed with Covid-19 in the postoperative period. PATIENTS AND METHODS: We performed 826 open cardiac surgeries in five tertiary centers. Most of the surgeries were elective coronary artery bypass grafting (CABG) (93.8%). A preoperative RT-PCR test and transcutaneous oxygen saturation were routinely investigated prior to surgery. We also investigated whether the patients already received Covid-19 treatment or had any contact with a Covid-19 patient in the last two weeks. We analyzed high sensitive C-reactive protein (hs-CRP), d-dimer, and fibrinogen, which plays a main role in the activation of procoagulant state after surgeries. RESULTS: Acute lung injury related to Covid-19 activation was observed in 48 out of 826 patients (5.8%). The median age of 48 patients was 63.9±12.4 years. Euro-Score and body mass index (BMI) were 6.1±1.1 and 29.2±4.1kg/m², respectively. RT-PCR test results were positive in 29 patients (60.4%). We performed thoracic computed tomography (CT) in all patients with or without positive RT-PCR test results. Thoracic CT images showed that there was a different degree of ARDS (mild, moderate, and serious). The median time of extracorporeal circulation (ECC) was 93.2±14.6 min. in on-pump surgery (IQR, 68-155 min.). Common symptoms included dyspnea (N = 22; 45.8%) and fever (N = 12; 25%). Eleven patients needed readmission to ICU. Compared with non-admitted to ICU patients, ICU patients were higher comorbidities and severe laboratory abnormalities (eg, high blood d-dimer and fibrinogen). We also detected significantly low oxygen saturation, hypercapnia, and severe acidosis in readmitted patients. Radiologic investigations showed that there were severe ARDS with bilateral pneumonic infiltration resistant to medical treatment in 6 out of 11 patients who died (54.5%). CONCLUSION: Diffuse pneumonic infiltration related to Covid-19 may develop in asymptomatic cardiac surgery patients with negative RT-PCR test results. Immunologic disorders resulting from ECC, physiologic distress, and anesthesia may activate Covid-19 during the incubation period. We need randomized clinical trials to explain Covid-19 activation in the latent period of the virus, and clinical outcomes in cardiac surgery.


Assuntos
Lesão Pulmonar Aguda/diagnóstico , Lesão Pulmonar Aguda/virologia , COVID-19/diagnóstico , COVID-19/virologia , Procedimentos Cirúrgicos Cardíacos , Período Pós-Operatório , Lesão Pulmonar Aguda/diagnóstico por imagem , Idoso , COVID-19/diagnóstico por imagem , Teste de Ácido Nucleico para COVID-19 , Cuidados Críticos , Feminino , Humanos , Achados Incidentais , Masculino , Pessoa de Meia-Idade , Readmissão do Paciente , Estudos Retrospectivos , SARS-CoV-2 , Estresse Fisiológico , Tomografia Computadorizada por Raios X , Ativação Viral
17.
Aging (Albany NY) ; 13(23): 24931-24942, 2021 12 12.
Artigo em Inglês | MEDLINE | ID: mdl-34897035

RESUMO

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.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Influenza Humana/diagnóstico , Reação em Cadeia da Polimerase Multiplex/métodos , Infecções por Vírus Respiratório Sincicial/diagnóstico , Adulto , Idoso , COVID-19/virologia , Feminino , Humanos , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Influenza Humana/virologia , Influenzavirus B/genética , Influenzavirus B/isolamento & purificação , Masculino , Pessoa de Meia-Idade , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sinciciais Respiratórios/genética , Vírus Sinciciais Respiratórios/isolamento & purificação , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Sensibilidade e Especificidade , Adulto Jovem
18.
PLoS One ; 16(12): e0260884, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34928966

RESUMO

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.


Assuntos
COVID-19/virologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2/genética , Carga Viral/métodos , Adolescente , Adulto , Idoso , COVID-19/mortalidade , Teste de Ácido Nucleico para COVID-19/métodos , Criança , Pré-Escolar , Feminino , Genoma Viral , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Sensibilidade e Especificidade , Adulto Jovem
19.
Nagoya J Med Sci ; 83(4): 883-891, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34916731

RESUMO

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.


Assuntos
Glândulas Suprarrenais/irrigação sanguínea , COVID-19/complicações , Infarto , Trombose/etiologia , Idoso , COVID-19/sangue , COVID-19/diagnóstico , Teste de Ácido Nucleico para COVID-19 , Feminino , Humanos , Infarto/etiologia , Infecções Respiratórias , SARS-CoV-2/isolamento & purificação
20.
Eur Rev Med Pharmacol Sci ; 25(23): 7607-7615, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34919261

RESUMO

Continuous rise in the number of COVID-19 cases, since it was first diagnosed in 2019, forced the entire medical fraternity to delay elective surgeries. The preoperative evaluation guidelines that were used in the pre-COVID-19 era underwent significant changes, adding modifications to meet the post-COVID patients' specific criteria and requirements. Currently, all patients before or at the time of hospital admission were tested using a nasopharyngeal swab, by RT-PCR for SARS-CoV-2. Apart from this, for a patient undergoing elective surgery in their post-COVID-19 period, it is mandatory to obtain a detailed history of COVID-19 disease/SARS-CoV-2 infection, to identify residual symptoms or any organ dysfunction the infection might have caused. As well as the functional optimization of the patient to achieve the best clinical and biological status before the surgery. After all the systems have been thoroughly investigated, the risk-benefit ratio needs to be calculated, keeping in mind the cytokine storm and inflammatory responses encountered postoperatively. A mere negative RT-PCR test cannot be considered as the only decisive factor to operate, as the post-COVID-19 phase can influence postoperative outcome of the patient. Hence, the pre-operative evaluation protocols of post-COVID patients should be set and followed thoroughly, in order to avoid post-surgical complications. For better surgical and post-surgical management of post-COVID-19 patients, conducting clinical tests, assessing previously administered medications, evaluating the need for deep venous thrombosis prophylaxes, and identifying subclinical inflammatory state are the measures that should be taken.


Assuntos
COVID-19/diagnóstico , Cuidados Pré-Operatórios/métodos , SARS-CoV-2/genética , Teste de Ácido Nucleico para COVID-19 , Procedimentos Cirúrgicos Eletivos , Humanos , Nasofaringe/virologia , Guias de Prática Clínica como Assunto
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