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1.
Indian J Gastroenterol ; 39(3): 236-242, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32875524

RESUMO

The outbreak of Corona Virus Disease-19 (COVID-19), caused by Severe Acute Respiratory Syndrome Corona Virus - 2 (SARS-CoV-2), a global pandemic, is having a significant impact on healthcare, especially the clinical microbiology laboratories all around the world. There are many reports which suggest that the disease can present with gastrointestinal symptoms such as nausea, vomiting, diarrhea, and loss of appetite, which the gastroenterologists may have to deal with. Hence, knowledge about the diagnosis of COVID-19 is important to gastroenterologists as well. The current review therefore covers the challenges faced while choosing appropriate sample collection, transport, and tests for SARS-CoV-2 infection. The right sample at the right time from the right anatomical site with the proper precautions is crucial in prompt and accurate diagnosis of COVID-19. The tests can be divided into direct, indirect, and complementary tests. In the direct test, real-time polymerase chain reaction (RT-PCR) assays are the molecular tests of choice for the diagnosis of COVID-19. Other direct tests include GeneXpert and TrueNAT. In indirect testing, antigen-antibody-based techniques are recommended for surveillance for the disease, which may help to formulate the control measures. Finally, the additional tests help in assessing the disease severity and evaluating the prognosis. All the above tests are important not only for diagnosis but also for management strategy and prognosis.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus , Pandemias , Pneumonia Viral , Técnicas de Laboratório Clínico/normas , Infecções por Coronavirus/sangue , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/epidemiologia , Humanos , Pneumonia Viral/sangue , Pneumonia Viral/diagnóstico , Pneumonia Viral/epidemiologia , Prognóstico , Reprodutibilidade dos Testes , Manejo de Espécimes/métodos , Manejo de Espécimes/normas
2.
BMC Med Res Methodol ; 20(1): 228, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917141

RESUMO

BACKGROUND: COVID-19, the disease caused by the highly infectious and transmissible coronavirus SARS-CoV-2, has quickly become a morbid global pandemic. Although the impact of SARS-CoV-2 infection in children is less clinically apparent, collecting high-quality biospecimens from infants, children, and adolescents in a standardized manner during the COVID-19 pandemic is essential to establish a biologic understanding of the disease in the pediatric population. This biorepository enables pediatric centers world-wide to collect samples uniformly to drive forward our understanding of COVID-19 by addressing specific pediatric and neonatal COVID-19-related questions. METHODS: A COVID-19 biospecimen collection study was implemented with strategic enrollment guidelines to include patients seen in urgent care clinics and hospital settings, neonates born to SARS-CoV-2 infected mothers, and asymptomatic children. The methodology described here, details the importance of establishing collaborations between the clinical and research teams to harmonize protocols for patient recruitment and sample collection, processing and storage. It also details modifications required for biobanking during a surge of the COVID-19 pandemic. RESULTS: Considerations and challenges facing enrollment of neonatal and pediatric cohorts are described. A roadmap is laid out for successful collection, processing, storage and database management of multiple pediatric samples such as blood, nasopharyngeal and oropharyngeal swabs, sputum, saliva, tracheal aspirates, stool, and urine. Using this methodology, we enrolled 327 participants, who provided a total of 972 biospecimens. CONCLUSIONS: Pediatric biospecimens will be key in answering questions relating to viral transmission by children, differences between pediatric and adult viral susceptibility and immune responses, the impact of maternal SARS-CoV-2 infection on fetal development, and factors driving the Multisystem Inflammatory Syndrome in Children. The specimens in this biorepository will allow necessary comparative studies between children and adults, help determine the accuracy of current pediatric viral testing techniques, in addition to, understanding neonatal exposure to SARS-CoV-2 infection and disease abnormalities. The successful establishment of a pediatric biorepository is critical to provide insight into disease pathogenesis, and subsequently, develop future treatment and vaccination strategies.


Assuntos
Betacoronavirus , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Manejo de Espécimes/métodos , Adolescente , Criança , Pré-Escolar , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/transmissão , Feminino , Desenvolvimento Fetal , Hospitalização , Humanos , Lactente , Recém-Nascido , Masculino , Pandemias , Pneumonia Viral/imunologia , Pneumonia Viral/transmissão
4.
6.
J Clin Virol ; 130: 104579, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32795959

RESUMO

BACKGROUND: Fast and reliable detection of SARS-CoV-2 is crucial for efficient control of the COVID-19 pandemic. Due to the high demand for SARS-CoV-2 testing there is a worldwide shortage of RNA extraction reagents. Therefore, extraction-free RT-qPCR protocols are urgently needed. OBJECTIVES: To establish a rapid RT-qPCR protocol for the detection of SARS-CoV-2 without the need of RNA extraction suitable for all respiratory materials. MATERIAL AND METHODS: Different SARS-CoV-2 positive respiratory materials from our routine laboratory were used as crude material after heat inactivation in direct RT-qPCR with the PrimeDirect™ Probe RT-qPCR Mix (TaKaRa). SARS-CoV-2 was detected using novel primers targeted to the E-gene. RESULTS: The protocol for the detection of SARS-CoV-2 in crude material used a prepared frozen-PCR mix with optimized primers and 5 µl of fresh, undiluted and pre-analytically heat inactivated respiratory material. For validation, 91 respiratory samples were analyzed in direct comparison to classical RNA-based RT-qPCR. Overall 81.3 % of the samples were detected in both assays with a strong correlation between both Ct values (r = 0.8492, p < 0.0001). The SARS-CoV-2 detection rate by direct RT-qPCR was 95.8 % for Ct values <35. All negative samples were characterized by low viral loads (Ct >35) and/or long storage times before sample processing. CONCLUSION: Direct RT-qPCR is a suitable alternative to classical RNA RT-qPCR, provided that only fresh samples (storage <1 week) are used. RNA extraction should be considered if samples have longer storage times or if PCR inhibition is observed. In summary, this protocol is fast, inexpensive and suitable for all respiratory materials.


Assuntos
Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/métodos , Sistema Respiratório/virologia , Manejo de Espécimes/métodos , Betacoronavirus , Infecções por Coronavirus/virologia , Primers do DNA/genética , Humanos , Pandemias , Pneumonia Viral/virologia , RNA Viral/análise , Sensibilidade e Especificidade , Fatores de Tempo
7.
J Clin Virol ; 131: 104570, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32805524

RESUMO

BACKGROUND: SARS-CoV-2 testing demand has outpaced its supply. Pooling samples for lower risk populations has the potential to accommodate increased demand for SARS-CoV-2 molecular testing. OBJECTIVE: To evaluate the sensitivity, specificity, and reproducibility of 4-way pooling of SARS-CoV-2 specimens for high-throughput RT-PCR. STUDY DESIGN: Individual samples were pooled 1:4 through automated liquid handling, extracted, and assayed by our emergency use authorized CDC-based RT-PCR laboratory developed test. Positive samples were serially diluted and theoretical and empirical PCR cycle thresholds were evaluated. Thirty-two distinct positive samples were pooled into negative specimens and individual CTs were compared to pooled CTs. Low positive samples were repeated for reproducibility and 32 four-way pools of negative specimens were assayed to determine specificity. RESULTS: Four-way pooling was associated with a loss of sensitivity of 1.7 and 2.0 CTs for our N1 and N2 targets, respectively. Pooling correctly identified SARS-CoV-2 in 94 % (n = 30/32) of samples tested. The two low positive specimens (neat CT > 35) not detected by pooling were individually repeated and detected 75 % (n=6/8) and 37.5 % (n = 3/8) of the time, respectively. All specimens individually determined negative were also negative by pooling. CONCLUSION: We report that 1:4 pooling of samples is specific and associated with an expected 2 CT loss in analytical sensitivity. Instead of running each sample individually, pooling of four samples will allow for a greater throughput and conserve scarce reagents.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Pneumonia Viral/diagnóstico , Manejo de Espécimes/métodos , Monitoramento Epidemiológico , Ensaios de Triagem em Larga Escala , Humanos , Pandemias , Reação em Cadeia da Polimerase , RNA Viral/isolamento & purificação , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
8.
J Clin Virol ; 131: 104593, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32823131

RESUMO

BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86 % & 100 % respectively while the negative percent agreement (NPA) was 100 % for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.


Assuntos
Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Sistema Respiratório/virologia , Saliva/virologia , Manejo de Espécimes/métodos , Adulto , Betacoronavirus , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Nasofaringe/virologia , Orofaringe/virologia , Pandemias , Faringe/virologia , Kit de Reagentes para Diagnóstico , Sensibilidade e Especificidade
10.
J Med Internet Res ; 22(9): e19471, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32790639

RESUMO

BACKGROUND: Innovative laboratory testing approaches for SARS-CoV-2 infection and immune response are needed to conduct research to establish estimates of prevalence and incidence. Self-specimen collection methods have been successfully used in HIV and sexually transmitted infection research and can provide a feasible opportunity to scale up SARS-CoV-2 testing for research purposes. OBJECTIVE: The aim of this study was to assess the willingness of adults to use different specimen collection modalities for themselves and children as part of a COVID-19 research study. METHODS: Between March 27 and April 1, 2020, we recruited 1435 adults aged 18 years or older though social media advertisements. Participants completed a survey that included 5-point Likert scale items stating how willing they were to use the following specimen collection testing modalities as part of a research study: home collection of a saliva sample, home collection of a throat swab, home finger-prick blood collection, drive-through site throat swab, clinic throat swab, and clinic blood collection. Additionally, participants indicated how the availability of home-based collection methods would impact their willingness to participate compared to drive-through and clinic-based specimen collection. We used Kruskal-Wallis tests and Spearman rank correlations to assess if willingness to use each testing modality differed by demographic variables and characteristics of interest. We compared the overall willingness to use each testing modality and estimated effect sizes with Cohen d. RESULTS: We analyzed responses from 1435 participants with a median age of 40.0 (SD=18.2) years and over half of which were female (761/1435, 53.0%). Most participants agreed or strongly agreed that they would be willing to use specimens self-collected at home to participate in research, including willingness to collect a saliva sample (1259/1435, 87.7%) or a throat swab (1191/1435, 83.1%). Willingness to collect a throat swab sample was lower in both a drive-through setting (64%) and clinic setting (53%). Overall, 69.0% (990/1435) of participants said they would be more likely to participate in a research study if they could provide a saliva sample or throat swab at home compared to going to a drive-through site; only 4.4% (63/1435) of participants said they would be less likely to participate using self-collected samples. For each specimen collection modality, willingness to collect specimens from children for research was lower than willingness to use on oneself, but the ranked order of modalities was similar. CONCLUSIONS: Most participants were willing to participate in a COVID-19 research study that involves laboratory testing; however, there was a strong preference for home specimen collection procedures over drive-through or clinic-based testing. To increase participation and minimize bias, epidemiologic research studies of SARS-CoV-2 infection and immune response should consider home specimen collection methods.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Manejo de Espécimes/métodos , Adulto , Infecções por Coronavirus/virologia , Feminino , Humanos , Masculino , Pandemias , Pneumonia Viral/virologia , Inquéritos e Questionários
11.
Indian J Pathol Microbiol ; 63(3): 350-357, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32769321

RESUMO

Declared as a pandemic by WHO on March 11, 2020, COVID-19 has brought about a dramatic change in the working of different laboratories across the country. Diagnostic laboratories testing different types of samples play a vital role in the treatment management. Irrespective of their size, each laboratory has to follow strict biosafety guidelines. Different sections of the laboratory receive samples that are variably infectious. Each sample needs to undergo a proper and well-designed processing system so that the personnel involved are not infected and also their close contacts. It takes a huge effort so as to limit the risk of exposure of the working staff during the collection, processing, reporting or dispatching of biohazard samples. Guidelines help in preventing the laboratory staff and healthcare workers from contracting the disease which has a known human to human route of transmission and high rate of mortality. A well-knit approach is the need of the hour to combat this fast spreading disease. We anticipate that the guidelines described in this article will be useful for continuing safe work practices by all the laboratories in the country.


Assuntos
Contenção de Riscos Biológicos/métodos , Infecções por Coronavirus/prevenção & controle , Infecções por Coronavirus/transmissão , Exposição Ocupacional/prevenção & controle , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Pneumonia Viral/transmissão , Manejo de Espécimes/métodos , Betacoronavirus , Desinfecção/métodos , Guias como Assunto , Substâncias Perigosas , Pessoal de Saúde/normas , Humanos , Laboratórios/normas , Patologistas/normas , Gerenciamento de Resíduos/métodos
12.
Biochem Med (Zagreb) ; 30(3): 030503, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32774121

RESUMO

The new corona virus SARS-CoV-2 (Severe Acute Respiratory Syndrome Corona Virus 2) causes a disease called COVID-19 (coronavirus disease 2019), that develops mostly in subjects with already impaired immune system function, primarily in the elderly and in individuals with some chronic disease or condition. The reasons for this should be sought in the processes of aging and chronic latent inflammation, i.e. immunosenescence and inflammaging. Laboratory medicine specialists are currently focused on proving the presence of the virus and defining biomarkers that would enable the prediction of disease progression. For now, it has been shown that useful biomarkers can include general biomarkers of inflammation (parameters of complete blood count, C-reactive protein, interleukin-6, procalcitonin), biomarkers of myocardial damage (high sensitivity troponin I/T, B-type natriuretic peptide, and N-terminal B type natriuretic peptide), and vascular biomarkers (D-dimer, prothrombin time, fibrinogen). Their actual diagnostic specificity, sensitivity and predictive value need to be tested on a larger number of subjects. In addition, it is important to find and evaluate specific biomarkers of immunosenescence.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/normas , Infecções por Coronavirus/sangue , Pessoal de Saúde/normas , Mediadores da Inflamação/sangue , Pneumonia Viral/sangue , Manejo de Espécimes/normas , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/metabolismo , Humanos , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/metabolismo , Manejo de Espécimes/métodos
13.
PLoS One ; 15(8): e0236775, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32756585

RESUMO

BACKGROUND: Options to increase the ease of testing for SARS-CoV-2 infection and immune response are needed. Self-collection of diagnostic specimens at home offers an avenue to allow people to test for SARS-CoV-2 infection or immune response without traveling to a clinic or laboratory. Before this study, survey respondents indicated willingness to self-collect specimens for COVID-related tests, but hypothetical willingness can differ from post-collection acceptability after participants collect specimens. METHODS: 153 US adults were enrolled in a study of the willingness and feasibility of patients to self-collect three diagnostic specimens (saliva, oropharyngeal swab (OPS) and dried blood spot (DBS) card) while observed by a clinician through a telehealth session. After the specimens were collected, 148 participants participated in a survey about the acceptability of the collection, packing and shipping process, and their confidence in the samples collected for COVID-related laboratory testing. RESULTS: A large majority of participants (>84%) reported that collecting, packing and shipping of saliva, OPS, and DBS specimens were acceptable. Nearly nine in 10 (87%) reported being confident or very confident that the specimens they collected were sufficient for laboratory analysis.There were no differences in acceptability for any specimen type, packing and shipping, or confidence in samples, by gender, age, race/ethnicity, or educational level. CONCLUSIONS: Self-collection of specimens for SARS-CoV-2 testing, and preparing and shipping specimens for analysis, were acceptable in a diverse group of US adults. Further refinement of materials and instructions to support self-collection of saliva, OPS and DBS specimens for COVID-related testing is needed.


Assuntos
Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Orofaringe/virologia , Cooperação do Paciente , Pneumonia Viral/diagnóstico , Saliva/virologia , Manejo de Espécimes/métodos , Adulto , Betacoronavirus/genética , Infecções por Coronavirus/virologia , Teste em Amostras de Sangue Seco/métodos , Escolaridade , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Pandemias , Cooperação do Paciente/etnologia , Pneumonia Viral/virologia , Autocuidado , Inquéritos e Questionários , Telemedicina
14.
BMC Infect Dis ; 20(1): 587, 2020 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-32770954

RESUMO

BACKGROUND: Tuberculosis (TB) is transmitted in bioaerosols containing Mycobacterium tuberculosis (Mtb). Despite being central to ongoing TB transmission, no routine diagnostic assay exists to measure Mtb in bioaerosols. Furthermore, published studies of Mtb in bioaerosol samples have been limited to individuals with sputum-positive pulmonary TB. Notably, TB diagnosis is based on clinical symptoms and sputum laboratory findings. This is despite the fact that approximately half of all patients commencing TB treatment are sputum-negative, resulting in a high proportion of presumptive treatments. Here, we propose to use a sensitive air sampling protocol to investigate the prevalence of Mtb-containing bioaerosols in both sputum-positive and sputum-negative TB suspects, at the same time evaluating the potential to identify unrecognized transmitters of TB. METHODS: Our parallel-group design will identify viable Mtb in bioaerosols produced by individuals attending a TB clinic in South Africa. Sampling will be performed on eligible individuals presenting with symptoms indicative of TB and repeated at 14 days if initially positive. Participants will be prospectively classified into three distinct groups based on National TB Control Program (NTBCP) criteria: Group A, TB notification with sputum-based laboratory confirmation; Group B, TB notification with empiric diagnosis; and Group C, individuals not notified. Group C individuals with detectable Mtb bioaerosol will be monitored until resolution of clinical and laboratory status. Collection of bioaerosol specimens will be via two consecutive sampling modalities: (1) direct sampling following a specific respiratory manoeuvre; and (2) indirect sampling during passive respiratory activity. Bioaerosol specimens will be analyzed for viable Mtb using DMN-trehalose staining and live-cell fluorescence microscopy. Mtb genomes and mycobacterial and host lipids will be detected using droplet digital PCR and mass spectrometry analyses, respectively. The primary objective is to determine the prevalence of Mtb bioaerosols in all TB clinic attendees and in each of the groups. Secondary objectives are to investigate differences in prevalence of Mtb bioaerosol by HIV status and current isoniazid preventive therapy (IPT) use; we will also determine the impact of anti-TB chemotherapy on Mtb-containing bioaerosol production. DISCUSSION: Respiratory bioaerosol has a potential role in non-invasive TB diagnosis, infectivity measurement and treatment monitoring. TRIAL REGISTRATION: ClinicalTrials.gov: NCT04241809 . Date of Registration: 27/1/2020.


Assuntos
Aerossóis/análise , Manejo de Espécimes/métodos , Tuberculose Pulmonar/diagnóstico , Adulto , DNA Bacteriano/química , DNA Bacteriano/metabolismo , Feminino , Humanos , Masculino , Espectrometria de Massas , Pessoa de Meia-Idade , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/isolamento & purificação , Reação em Cadeia da Polimerase , África do Sul , Escarro/microbiologia
15.
BMC Infect Dis ; 20(1): 594, 2020 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-32787869

RESUMO

BACKGROUND: Implementation of an effective Tuberculosis Routine Surveillance System in low-income countries like Tanzania is problematic, despite being an essential tool for the detection and effective monitoring of drug resistant tuberculosis. Long delays in specimen transportation from the facilities to reference laboratory and results dissemination back to the health facilities, result in poor patient management, particularly where multidrug-resistant tuberculosis disease is present. METHODS: Following a detailed qualitative study, a pilot intervention of a revised Tuberculosis Routine Surveillance System was implemented in Mwanza region, Tanzania. This included the use of rapid molecular methods for the detection of both tuberculosis and drug resistance using Xpert MTB/RIF in some Mwanza sites, the use of Xpert MTB/RIF and Line Probe Assay at the Central Tuberculosis Reference Laboratory, a revised communication strategy and interventions to address the issue of poor form completion. A before and after comparison of the intervention on the number of drug resistant tuberculosis cases identified and the time taken for results feedback to the requesting site was reported. RESULTS: The revised system for previously treated cases tested at the Central Reference Laboratory was able to obtain the following findings; the number of cases tested increased from 75 in 2016 to 185 in 2017. The times for specimen transportation from health facilities to the reference laboratory were reduced by 22% (from 9 to 7 days). The median time for the district to receive results was reduced by 36% (from 11 to 7 days). Overall the number of drug resistant tuberculosis cases starting treatment increased by 67% (from 12 to 20). CONCLUSION: Detection of drug resistance could significantly be enhanced, and delays reduced by introduction of new technologies and improved routine surveillance system, including better communication using mobile applications such as 'WhatsApp' and close follow-ups. A larger scale study is now merited to ascertain if these benefits are robust across different contexts.


Assuntos
Diagnóstico Tardio/prevenção & controle , Testes Diagnósticos de Rotina/métodos , Monitoramento Epidemiológico , Mycobacterium tuberculosis/genética , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico , Tuberculose Resistente a Múltiplos Medicamentos/epidemiologia , Antibióticos Antituberculose/uso terapêutico , Comunicação , Farmacorresistência Bacteriana Múltipla , Instalações de Saúde , Humanos , Laboratórios , Mycobacterium tuberculosis/isolamento & purificação , Técnicas de Amplificação de Ácido Nucleico/métodos , Projetos Piloto , Estudos Prospectivos , Pesquisa Qualitativa , Rifampina/uso terapêutico , Manejo de Espécimes/métodos , Tanzânia/epidemiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico
17.
PLoS One ; 15(8): e0237127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32756602

RESUMO

BACKGROUND: The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. METHODS: We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay. RESULTS: Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%). CONCLUSION: We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Staphylococcus aureus Resistente à Meticilina/genética , Pneumonia Viral/diagnóstico , Manejo de Espécimes/métodos , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/virologia , Humanos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Nasofaringe/microbiologia , Nasofaringe/virologia , Pandemias , Pneumonia Viral/virologia , Estabilidade de RNA , RNA Bacteriano/análise , RNA Bacteriano/metabolismo , RNA Viral/análise , RNA Viral/metabolismo , Reação em Cadeia da Polimerase em Tempo Real
18.
PLoS One ; 15(8): e0238417, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32857823

RESUMO

The rapid global spread of the coronavirus disease (COVID-19) has inflicted significant health and socioeconomic burden on affected countries. As positive cases continued to rise in Malaysia, public health laboratories experienced an overwhelming demand for COVID-19 screening. The confirmation of positive cases of COVID-19 has solely been based on the detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) using real-time reverse transcription polymerase chain reaction (qRT-PCR). In efforts to increase the cost-effectiveness and efficiency of COVID-19 screening, we evaluated the feasibility of pooling clinical Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens during nucleic acid extraction without a reduction in sensitivity of qRT-PCR. Pools of 10 specimens were extracted and subsequently tested by qRT-PCR according to the WHO-Charité protocol. We demonstrated that the sample pooling method showed no loss of sensitivity. The effectiveness of the pooled testing strategy was evaluated on both retrospective and prospective samples, and the results showed a similar detection sensitivity compared to testing individual sample alone. This study demonstrates the feasibility of using a pooled testing strategy to increase testing capacity and conserve resources, especially when there is a high demand for disease testing.


Assuntos
Infecções por Coronavirus/diagnóstico , Programas de Rastreamento/métodos , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real , Manejo de Espécimes/métodos , Betacoronavirus , Humanos , Malásia , Nasofaringe/virologia , Orofaringe/virologia , Pandemias , Sensibilidade e Especificidade
19.
Methods Mol Biol ; 2203: 41-53, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32833202

RESUMO

Wild birds are natural hosts of multiple microbial agents, including a wide diversity of coronaviruses. Here we describe a pan-Coronavirus detection RT-PCR method to identify those viruses regardless of the coronavirus genus or nature of the specimen. We also describe a protocol using high-throughput sequencing technologies to obtain their entire genome, which overcomes the inherent difficulties of wild bird coronavirus sequencing, that is, their genetic diversity and the lack of virus isolation methods.


Assuntos
Doenças das Aves/virologia , Infecções por Coronavirus/veterinária , Coronavirus/genética , Coronavirus/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/métodos , Animais , Animais Selvagens , Infecções por Coronavirus/genética , RNA Replicase/genética , Manejo de Espécimes/métodos
20.
ACS Infect Dis ; 6(9): 2319-2336, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32786280

RESUMO

In December 2019, a novel beta (ß) coronavirus eventually named SARS-CoV-2 emerged in Wuhan, Hubei province, China, causing an outbreak of severe and even fatal pneumonia in humans. The virus has spread very rapidly to many countries across the world, resulting in the World Health Organization (WHO) to declare a pandemic on March 11, 2020. Clinically, the diagnosis of this unprecedented illness, called coronavirus disease-2019 (COVID-19), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. Therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain SARS-CoV-2 at clinical and population level. Here, we summarize the main clinical and imaging findings of COVID-19 patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for SARS-CoV-2 diagnosis.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Infecções por Coronavirus/virologia , Humanos , Microscopia Eletrônica , Pandemias , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase/métodos , Análise de Sequência , Testes Sorológicos/métodos , Manejo de Espécimes/métodos
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