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1.
Virol J ; 19(1): 168, 2022 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-36303187

RESUMO

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.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , Mutação Puntual , Pandemias , COVID-19/diagnóstico , Reação em Cadeia da Polimerase , Mutação
2.
BMC Infect Dis ; 20(1): 745, 2020 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-33046011

RESUMO

BACKGROUND: Workers and residents in Care Homes are considered at special risk for the acquisition of SARS-CoV-2 infection, due to the infectivity and high mortality rate in the case of residents, compared to other containment areas. The role of presymptomatic people in transmission has been shown to be important and the early detection of these people is critical for the control of new outbreaks. Pooling strategies have proven to preserve SARS-CoV-2 testing resources. The aims of the present study, based in our local experience, were (a) to describe SARS-CoV-2 prevalence in institutionalized people in Galicia (Spain) during the Coronavirus pandemic and (b) to evaluate the expected performance of a pooling strategy using RT-PCR for the next rounds of screening of institutionalized people. METHODS: A total of 25,386 Nasopharyngeal swab samples from the total of the residents and workers at Care Homes in Galicia (March to May 2020) were individually tested using RT-PCR. Prevalence and quantification cycle (Cq) value distribution of positives was calculated. Besides, 26 pools of 20 samples and 14 pools of 5 samples were tested using RT-PCR as well (1 positive/pool). Pooling proof of concept was performed in two populations with 1.7 and 2% prevalence. RESULTS: Distribution of SARS-CoV-2 infection at Care Homes was uneven (0-60%). As the virus circulation global rate was low in our area (3.32%), the number of people at risk of acquiring the infection continues to be very high. In this work, we have successfully demonstrated that pooling of different groups of samples at low prevalence clusters, can be done with a small average delay on Cq values (5 and 2.85 cycles for pools of 20 and 5 samples, respectively). CONCLUSIONS: A new screening system with guaranteed protection is required for small clusters, previously covered with individual testing. Our proposal for Care Homes, once prevalence zero is achieved, would include successive rounds of testing using a pooling solution for transmission control preserving testing resources. Scale-up of this method may be of utility to confront larger clusters to avoid the viral circulation and keeping them operative.


Assuntos
Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/prevenção & controle , Casas de Saúde/estatística & dados numéricos , Pandemias/prevenção & controle , Pneumonia Viral/diagnóstico , Pneumonia Viral/prevenção & controle , COVID-19 , Teste para COVID-19 , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Surtos de Doenças/prevenção & controle , Surtos de Doenças/estatística & dados numéricos , Humanos , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , Espanha/epidemiologia
3.
PLoS One ; 19(4): e0289188, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38683803

RESUMO

To control the SARS-CoV-2 pandemic, healthcare systems have focused on ramping up their capacity for epidemiological surveillance through viral whole genome sequencing. In this paper, we tested the performance of two protocols of SARS-CoV-2 nucleic acid enrichment, an amplicon enrichment using different versions of the ARTIC primer panel and a hybrid-capture method using KAPA RNA Hypercap. We focused on the challenge of the Omicron variant sequencing, the advantages of automated library preparation and the influence of the bioinformatic analysis in the final consensus sequence. All 94 samples were sequenced using Illumina iSeq 100 and analysed with two bioinformatic pipelines: a custom-made pipeline and an Illumina-owned pipeline. We were unsuccessful in sequencing six samples using the capture enrichment due to low reads. On the other hand, amplicon dropout and mispriming caused the loss of mutation G21987A and the erroneous addition of mutation T15521A respectively using amplicon enrichment. Overall, we found high sequence agreement regardless of method of enrichment, bioinformatic pipeline or the use of automation for library preparation in eight different SARS-CoV-2 variants. Automation and the use of a simple app for bioinformatic analysis can simplify the genotyping process, making it available for more diagnostic facilities and increasing global vigilance.


Assuntos
COVID-19 , Sequenciamento de Nucleotídeos em Larga Escala , SARS-CoV-2 , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Humanos , COVID-19/epidemiologia , COVID-19/virologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genoma Viral , RNA Viral/genética , Mutação , Monitoramento Epidemiológico , Biologia Computacional/métodos , Sequenciamento Completo do Genoma/métodos
4.
Infect Dis (Lond) ; : 1-13, 2024 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-39046827

RESUMO

BACKGROUND: To infer a reliable SARS-CoV-2 antibody protection level from a serological test, an appropriate quantitative threshold and solid equivalence across serological tests are needed. Additionally, tests should show a solid correlation with neutralising assays and with the protection observed in large population cohorts even against emerging variants. OBJECTIVES: We studied convalescent and vaccinated populations using 11 commercial antibody assays. Results were compared to evaluate discrepancies across tests. Neutralisation capacity was measured in a subset of the samples with a lentiviral-based assay. METHODS: Serum from convalescent (n = 121) and vaccinated individuals (n = 471, 260 with Comirnaty, 110 with Spikevax, and 96 with Vaxzevria) was assessed using 11 different assays, including two from Abbott, Euroimmun, Liaison, Roche, and Vircell, and one from Siemens. A spike protein-lentiviral vector with a fluorescent reporter was used for neutralisation assay of serum from convalescent (n = 26) and vaccinated (n = 39) individuals. RESULTS: Positivity ranged between 81.3 and 94.3% after infection and 99.4 and 99.7% after vaccination, depending on the assay. Both cohorts showed a high level of qualitative agreement across tests (Fleiss' kappa = 0.598 and 0.719 for convalescent and vaccinated respectively). Spikevax vaccine recipients showed the highest level of antibodies in all tests. Effectiveness of each test predicting SARS-CoV-2 neutralising capacity depended on assay type and target, with CLIA and anti-S being more effective than ELISA and anti-N assays, respectively. CONCLUSIONS: High-throughput immunoassays are good predictors of neutralising capacity. Updated targets and better standardisation would be required to find an effective correlate of protection, especially to account for antibodies against new variants.

5.
Sci Rep ; 13(1): 7786, 2023 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-37179356

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been and remains one of the major challenges modern society has faced thus far. Over the past few months, large amounts of information have been collected that are only now beginning to be assimilated. In the present work, the existence of residual information in the massive numbers of rRT-PCRs that tested positive out of the almost half a million tests that were performed during the pandemic is investigated. This residual information is believed to be highly related to a pattern in the number of cycles that are necessary to detect positive samples as such. Thus, a database of more than 20,000 positive samples was collected, and two supervised classification algorithms (a support vector machine and a neural network) were trained to temporally locate each sample based solely and exclusively on the number of cycles determined in the rRT-PCR of each individual. Overall, this study suggests that there is valuable residual information in the rRT-PCR positive samples that can be used to identify patterns in the development of the SARS-CoV-2 pandemic. The successful application of supervised classification algorithms to detect these patterns demonstrates the potential of machine learning techniques to aid in understanding the spread of the virus and its variants.


Assuntos
COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Algoritmos , Aprendizado de Máquina , Teste para COVID-19
6.
Enferm Infecc Microbiol Clin ; 24(9): 541-5, 2006 Nov.
Artigo em Espanhol | MEDLINE | ID: mdl-17125671

RESUMO

OBJECTIVE: The aim of this study is to assess a real-time PCR technique on the LightCycler 2.0 with SYBR-Green I detection as compared to another real-time PCR method based on detection with FRET (fluorescence resonance energy transfer) probes for the quantification of CMV DNA. METHODS: The two real-time PCR methods were used to test plasma samples from immunocompromised patients with clinically suspected CMV disease, patients under follow-up without symptoms, and healthy adults. A standard curve for quantitative analysis by the SYBR-Green I method was performed with 10-fold diluted solutions of DNA from the CMV Towne strain (ATCC VR-977) cultured in MRC-5 monolayer. In addition, frozen samples from patients positive for CMV pp65 antigenemia were also analyzed and results compared using the two real time PCR methods. RESULTS: The real-time PCR technique using SYBR-Green I on the LightCycler 2.0 was a highly specific, fast, simple and reliable test to quantify CMV; moreover, it was cost-effective. CONCLUSION: Quantification of CMV DNA in plasma using this sensitive, fast, low-cost method was advantageous for the diagnosis and follow up of patients with opportunistic CMV infection, which are increasingly more frequent in our daily hospital clinical practice.


Assuntos
Antígenos Virais/sangue , Sistemas Computacionais , Infecções por Citomegalovirus/sangue , DNA Viral/sangue , Corantes Fluorescentes/análise , Infecções Oportunistas/sangue , Compostos Orgânicos/análise , Reação em Cadeia da Polimerase/métodos , Viremia/sangue , Infecções Oportunistas Relacionadas com a AIDS/sangue , Infecções Oportunistas Relacionadas com a AIDS/diagnóstico , Infecções Oportunistas Relacionadas com a AIDS/virologia , Adulto , Benzotiazóis , Transplante de Medula Óssea , Linhagem Celular , Criança , Sistemas Computacionais/economia , Citomegalovirus/genética , Citomegalovirus/imunologia , Citomegalovirus/isolamento & purificação , Infecções por Citomegalovirus/diagnóstico , Infecções por Citomegalovirus/virologia , Diaminas , Transferência Ressonante de Energia de Fluorescência , Humanos , Hospedeiro Imunocomprometido , Recém-Nascido , Neoplasias/complicações , Neutrófilos/virologia , Infecções Oportunistas/diagnóstico , Infecções Oportunistas/virologia , Fosfoproteínas/sangue , Reação em Cadeia da Polimerase/economia , Reação em Cadeia da Polimerase/instrumentação , Reação em Cadeia da Polimerase/normas , Complicações Pós-Operatórias/sangue , Complicações Pós-Operatórias/diagnóstico , Complicações Pós-Operatórias/virologia , Quinolinas , Kit de Reagentes para Diagnóstico , Padrões de Referência , Sensibilidade e Especificidade , Proteínas da Matriz Viral/sangue , Viremia/diagnóstico , Viremia/virologia
7.
Enferm Infecc Microbiol Clin ; 21(9): 472-6, 2003 Nov.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-14572378

RESUMO

INTRODUCTION: Aspergillus fumigatus is a filamentous fungus that acts as an opportunistic pathogen and has emerged as a major problem in immunosuppressed patients. Nosocomial outbreaks of aspergillosis are becoming more frequent, but their identification and epidemiological characterization is slow and difficult. OBJECTIVE: Description of a fast, sensitive, specific method to identify and fingerprint A. fumigatus using methodology available in clinical laboratories. METHODS: We studied several strains of A. fumigatus isolated from patients with invasive aspergillosis (n = 4), the hospital environment (n = 5) and reference cultures (n = 1), as well as other close phylogenetic fungal species from patients (n = 1), hospital environment (n = 6) and reference cultures (n = 1). A. fumigatus was identified by both touchdown PCR and conventional phenotyping methods. Genotyping was performed with random amplification of polymorphic DNA (RAPD) analysis, comparing the results from two primers (OPZ-19 and R-108) and different amplification protocols with regard to band resolution and reproducibility. RESULTS: Touchdown PCR and phenotype results were identical. Best RAPD results were obtained with the R-108 primer and considerably longer ramp times between annealing and extension. CONCLUSION: RAPD analysis is a fast, reliable tool for DNA fingerprinting. Patterns may be easier to repeat and interpret when longer ramp times are used. Touchdown PCR combined with RAPD analysis is a sensitive, accurate method for managing clinical outbreaks of Aspergillus fumigatus.


Assuntos
Aspergilose/diagnóstico , Aspergillus fumigatus/isolamento & purificação , Infecção Hospitalar/diagnóstico , Técnicas de Tipagem Micológica , Reação em Cadeia da Polimerase , Técnica de Amplificação ao Acaso de DNA Polimórfico , Aspergilose/epidemiologia , Aspergilose/microbiologia , Aspergillus fumigatus/classificação , Aspergillus fumigatus/genética , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , DNA Fúngico/análise , Genótipo , Humanos , Infecções Oportunistas/diagnóstico , Infecções Oportunistas/epidemiologia , Infecções Oportunistas/microbiologia , Especificidade da Espécie , Fatores de Tempo
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