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1.
J Med Virol ; 94(1): 147-153, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34411312

RESUMO

This study aimed to determine the frequency of SARS-CoV-2 RNA in serum and its association with the clinical severity of COVID-19. This retrospective cohort study performed at Toyama University Hospital included consecutive patients with confirmed COVID-19. The prevalence of SARS-CoV-2 RNAemia and the strength of its association with clinical severity variables were examined. Fifty-six patients were included in this study. RNAemia was detected in 19.6% (11/56) patients on admission, and subsequently in 1.0% (1/25), 50.0% (6/12), and 100.0% (4/4) moderate, severe, and critically ill patients, respectively. Patients with RNAemia required more frequent oxygen supplementation (90.0% vs. 13.3%), ICU admission (81.8% vs. 6.7%), and invasive mechanical ventilation (27.3% vs. 0.0%). Among patients with RNAemia, the median viral loads of nasopharyngeal (NP) swabs that were collected around the same time as the serum sample were significantly higher in critically ill (5.4 log10 copies/µl; interquartile range [IQR]: 4.2-6.3) than in moderate-severe cases (2.6 log10 copies/µl; [IQR: 1.1-4.5]; p = 0.030) and were significantly higher in nonsurvivors (6.2 log10 copies/µl [IQR: 6.0-6.5]) than in survivors (3.9 log10 copies/µl [IQR: 1.6-4.6]; p = 0.045). This study demonstrated a relatively high proportion of SARS-CoV-2 RNAemia and an association between RNAemia and clinical severity. Moreover, among the patients with RNAemia, the viral loads of NP swabs were correlated with disease severity and mortality, suggesting the potential utility of combining serum testing with NP tests as a prognostic indicator for COVID-19, with higher quality than each separate test.


Assuntos
COVID-19/virologia , Nasofaringe/virologia , RNA Viral/sangue , SARS-CoV-2/isolamento & purificação , Carga Viral , Viremia , Adolescente , Adulto , Idoso , COVID-19/mortalidade , COVID-19/fisiopatologia , Criança , Estado Terminal , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Estudos Retrospectivos , Índice de Gravidade de Doença , Adulto Jovem
2.
J Med Virol ; 94(1): 327-334, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34524690

RESUMO

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in COVID-19 pandemic control and elimination efforts, especially by elucidating its global transmission network and illustrating its viral evolution. The deployment of multiplex PCR assays that target SARS-CoV-2 followed by either massively parallel or nanopore sequencing is a widely-used strategy to obtain genome sequences from primary samples. However, multiplex PCR-based sequencing carries an inherent bias of sequencing depth among different amplicons, which may cause uneven coverage. Here we developed a two-pool, long-amplicon 36-plex PCR primer panel with ~1000-bp amplicon lengths for full-genome sequencing of SARS-CoV-2. We validated the panel by assessing nasopharyngeal swab samples with a <30 quantitative reverse transcription PCR cycle threshold value and found that ≥90% of viral genomes could be covered with high sequencing depths (≥20% mean depth). In comparison, the widely-used ARTIC panel yielded 79%-88% high-depth genome regions. We estimated that ~5 Mbp nanopore sequencing data may ensure a >95% viral genome coverage with a ≥10-fold depth and may generate reliable genomes at consensus sequence levels. Nanopore sequencing yielded false-positive variations with frequencies of supporting reads <0.8, and the sequencing errors mostly occurred on the 5' or 3' ends of reads. Thus, nanopore sequencing could not elucidate intra-host viral diversity.


Assuntos
Genoma Viral/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Sequenciamento por Nanoporos/métodos , SARS-CoV-2/genética , Sequenciamento Completo do Genoma/métodos , COVID-19 , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Nasofaringe/virologia , RNA Viral/genética , Análise de Sequência de RNA/métodos
3.
J Med Virol ; 94(1): 417-423, 2022 01.
Artigo em Inglês | MEDLINE | ID: mdl-34581458

RESUMO

A 36-year-old male with diffuse large B-cell lymphoma on maintenance rituximab therapy presented to the emergency department with high fever and fatigue. A chest X-ray showed a lobar infiltrate, 40 days before admission the patient suffered from a mild coronavirus disease 2019 (COVID-19) infection and fully recovered. PCR nasopharyngeal swab was negative for COVID-19. Comprehensive biochemical, radiological, and pathological evaluation including 18-fluorodeoxyglucose positron emission tomography with computed tomography and transbronchial lung biopsy found no pathogen or lymphoma recurrence. Treatment for pneumonia with antibiotic and antifungal agents was nonbeneficial. A diagnosis of secondary organizing pneumonia (OP) was made after pneumonia migration and a rapid response to corticosteroids. OP secondary to a viral respiratory infection has been well described. Raising awareness for post-COVID-19 OP has therapeutic and prognostic importance because those patients benefit from steroid therapy. We believe the condition described here is underdiagnosed and undertreated by doctors worldwide. Because of the ongoing global pandemic we are now encountering a new kind of patient, patients that have recovered from COVID-19. We hope that this case may contribute to gaining more knowledge about this growing patient population.


Assuntos
Corticosteroides/uso terapêutico , COVID-19/terapia , Pneumonia em Organização Criptogênica/diagnóstico , Pneumonia em Organização Criptogênica/tratamento farmacológico , Adulto , Antineoplásicos Imunológicos/uso terapêutico , Pneumonia em Organização Criptogênica/patologia , Humanos , Hospedeiro Imunocomprometido/imunologia , Linfoma Difuso de Grandes Células B/tratamento farmacológico , Masculino , Nasofaringe/virologia , Tomografia por Emissão de Pósitrons , Rituximab/uso terapêutico , SARS-CoV-2
4.
Indian J Tuberc ; 68(4): 450-456, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34752312

RESUMO

BACKGROUND: Moderate and severe COVID-19 patients typically present with pneumonia. In this study we aimed to detect the occurrence of pulmonary residuals as a late sequela of COVID-19 and to identify it's predictors among moderate and severe cases. METHODS: This observational prospective study involved 85 COVID-19 patients confirmed by real time polymerase chain reaction (RT-PCR) nasopharyngeal swab, patients were recruited in the period of 1 st of June to 1 st of July. Demographic and clinical data were obtained for each patient. Chest imaging was performed initially and after 3 weeks to detect post COVID pulmonary residuals. RESULTS: The study population included 74 (87.1%) moderate and 11 (12.9%) severe patients. Patients with older age, male gender, high BMI and initial chest CT of consolidation/mixed consolidation and ground glass opacities (GGOs) had more frequent post COVID-19 pulmonary residuals (P 0.003, 0.026, 0.031, 0.035) respectively. There was a statistically significant difference between patients who showed complete resolution and patients who developed pulmonary residuals regarding the lymphocyte count, serum CRP and ferritin levels (P 0.0001). After logistic regression, male gender, high BMI, initial chest CT of consolidation/mixed consolidation and GGOs, lymphocytopenia, high serum CRP and ferritin levels were the predictors of pulmonary residuals. While the age wasn't statistically significant. CONCLUSION: 38.5% of moderate and severe COVID-19 patients tend to have pulmonary residuals. Independent predictors of pulmonary residuals as a sequela of COVID-19 are male gender, high BMI, initial chest CT of consolidation and mixed consolidation/GGOs, lymphocytopenia, high serum CRP and ferritin levels.


Assuntos
COVID-19/complicações , COVID-19/diagnóstico por imagem , Pulmão/diagnóstico por imagem , Fibrose Pulmonar/epidemiologia , SARS-CoV-2/isolamento & purificação , Tórax/diagnóstico por imagem , Adulto , Idoso , COVID-19/epidemiologia , COVID-19/terapia , Teste de Ácido Nucleico para COVID-19 , Humanos , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Estudos Prospectivos , Fibrose Pulmonar/diagnóstico por imagem , Reação em Cadeia da Polimerase em Tempo Real , SARS-CoV-2/genética , Tomografia Computadorizada por Raios X/métodos , Resultado do Tratamento
5.
Sci Rep ; 11(1): 21658, 2021 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-34737323

RESUMO

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , SARS-CoV-2/genética , COVID-19/genética , Teste de Ácido Nucleico para COVID-19/economia , Teste para COVID-19/métodos , Proteínas do Nucleocapsídeo de Coronavírus/genética , Primers do DNA , Eletroforese em Gel de Ágar/métodos , Humanos , Laboratórios , Nasofaringe/virologia , RNA Viral/genética , Ribonuclease P/genética , Ribonuclease P/metabolismo , SARS-CoV-2/patogenicidade , Sensibilidade e Especificidade
6.
J Korean Med Sci ; 36(44): e301, 2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34783217

RESUMO

We used serial rectal swabs to investigate the amount and duration of virus secretion through the gastrointestinal tract and assessed the association between fecal shedding and gastrointestinal symptoms and to clarify the clinical usefulness testing rectal swabs. We enrolled ten adult patients hospitalized with symptomatic coronavirus disease 2019 (COVID-19). Respiratory and stool specimens were collected by physicians. The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed using real-time reverse-transcription polymerase chain reaction. All ten patients had respiratory symptoms, six had diarrhea, and seven were positive for SARS-CoV-2 on rectal swabs. The viral loads in the respiratory specimens was higher than those in the rectal specimens, and no rectal specimens were positive after the respiratory specimens became negative. There was no association between gastrointestinal symptoms, pneumonia, severity, and rectal viral load. Rectal swabs may play a role in detecting SARS-CoV-2 in individuals with suspected COVID-19, regardless of gastrointestinal symptoms.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/virologia , Reto/virologia , SARS-CoV-2/isolamento & purificação , Eliminação de Partículas Virais , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/complicações , COVID-19/transmissão , Diarreia/etiologia , Diarreia/virologia , Fezes/virologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Estudos Prospectivos , Reação em Cadeia da Polimerase em Tempo Real , Índice de Gravidade de Doença , Fatores de Tempo , Carga Viral
7.
J Infect Dev Ctries ; 15(10): 1376-1383, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34780358

RESUMO

INTRODUCTION: The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed. The virus has been constantly mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS-CoV-2 have been defined globally. In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants. METHODOLOGY: The real time PCR was performed on nasopharyngeal specimen to confirm SARS-CoV-2 with Orf 1ab and E gene as targets. The virus isolates were sequenced through oxford nanopore technology MinION platform. Isolates from the first and second wave of COVID-19 outbreak in Karachi were compared. RESULTS: The overall positivity rate for PCR was 26.24% with the highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19. CONCLUSIONS: Based on the present findings it is suggested that the locally transmitted virus from Karachi varies from those reported from other parts of Pakistan. Slight variability was also observed between viruses from the first and second wave. Variability in any potential vaccine target may result in failed trials, therefore information on any local viral variants is always useful for effective vaccine design and/or selection.


Assuntos
COVID-19/transmissão , Genoma Viral , Nanoporos , Nasofaringe/virologia , SARS-CoV-2/genética , Sequenciamento Completo do Genoma/métodos , Adulto , COVID-19/epidemiologia , COVID-19/virologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Paquistão , Filogenia , Reação em Cadeia da Polimerase , Sequenciamento Completo do Genoma/instrumentação , Adulto Jovem
8.
J Infect Dev Ctries ; 15(10): 1408-1414, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34780363

RESUMO

INTRODUCTION: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. METHODOLOGY: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. RESULTS: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson's r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. CONCLUSIONS: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.


Assuntos
COVID-19/virologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2/genética , Carga Viral/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/diagnóstico por imagem , Criança , Pré-Escolar , Estudos Transversais , Feminino , Humanos , Pulmão/diagnóstico por imagem , Pulmão/patologia , Pulmão/virologia , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Orofaringe/diagnóstico por imagem , Estudos Retrospectivos , Tomografia Computadorizada por Raios X , Adulto Jovem
9.
J Biosci ; 462021.
Artigo em Inglês | MEDLINE | ID: mdl-34728592

RESUMO

The rapid spread and evolution of various strains of SARS-CoV-2, the virus responsible for COVID-19, continues to challenge the disease controlling measures globally. Alarming concern is, the number of second wave infections surpassed the first wave and the onset of severe symptoms manifesting rapidly. In this scenario, testing of maximum population in less time and minimum cost with existing diagnostic amenities is the only possible way to control the spread of the virus. The previously described RNA extraction-free methods using dry swab have been shown to be advantageous in these critical times by different studies. In this work, we show the temporal stability and performance of the dry swab viral detection method at two different temperatures. Contrived dry swabs holding serially diluted SARS-CoV-2 strains A2a and A3i at 25°C (room temperature; RT) and 4°C were subjected to direct RT-PCR and compared with standard VTM-RNA based method. The results clearly indicate that dry swab method of RNA detection is as efficient as VTM-RNA-based method in both strains, when checked for up to 72 h. The lesser CT values of dry swab samples in comparison to that of the VTM-RNA samples suggest better sensitivity of the method within 48 h of time. The results collectively suggest that dry swab samples are stable at RT for 24 h and the detection of SARS-CoV-2 RNA by RT-PCR do not show variance from VTM-RNA. This extraction free, direct RT-PCR method holds phenomenal standing in the present life-threatening circumstances due to SARS-CoV-2.


Assuntos
Teste para COVID-19/métodos , COVID-19/diagnóstico , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , SARS-CoV-2/genética , Manejo de Espécimes/métodos , COVID-19/virologia , Teste para COVID-19/normas , Humanos , Nasofaringe/virologia , Preservação Biológica/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , SARS-CoV-2/classificação , Sensibilidade e Especificidade , Temperatura
11.
Sci Rep ; 11(1): 20323, 2021 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-34645907

RESUMO

This study aimed to develop a highly sensitive SARS-CoV-2 nucleocapsid antigen assay using the single molecule array (Simoa) technology and compare it with real time RT-PCR as used in routine clinical practice with the ambition to achieve a comparative technical and clinical sensitivity. Samples were available from 148 SARS-CoV-2 real time RT-PCR positive and 73 SARS-CoV-2 real time RT-PCR negative oropharyngeal swabs. For determination of technical sensitivity SARS-CoV-2 virus culture material was used. The samples were treated with lysis buffer and analyzed using both an in-house and a pre-commercial SARS-CoV-2 nucleocapsid antigen assay on Simoa. Both nucleocapsid antigen assays have a technical sensitivity corresponding to around 100 SARS-CoV-2 RNA molecules/mL. Using a cut-off at 0.1 pg/mL the pre-commercial SARS-CoV-2 nucleocapsid antigen assay had a sensitivity of 96% (95% CI 91.4-98.5%) and specificity of 100% (95% CI 95.1-100%). In comparison the in-house nucleocapsid antigen assay had sensitivity of 95% (95% CI 89.3-98.1%) and a specificity of 100% (95% CI 95.1-100%) using a cut-off at 0.01 pg/mL. The two SARS-CoV-2 nucleocapsid antigen assays correlated with r = 0.91 (P < 0.0001). The in-house and the pre-commercial SARS-CoV-2 nucleocapsid antigen assay demonstrated technical and clinical sensitivity comparable to real-time RT-PCR methods for identifying SARS-CoV-2 infected patients and thus can be used clinically as well as serve as a reference method for antigen Point of Care Testing.


Assuntos
COVID-19/diagnóstico , Proteínas do Nucleocapsídeo de Coronavírus/imunologia , SARS-CoV-2/imunologia , Antígenos Virais/imunologia , Teste Sorológico para COVID-19/métodos , Proteínas do Nucleocapsídeo de Coronavírus/análise , Dinamarca , Testes Diagnósticos de Rotina , Humanos , Técnicas Imunoenzimáticas , Nasofaringe/virologia , Nucleocapsídeo/análise , Nucleocapsídeo/imunologia , Fosfoproteínas/análise , Fosfoproteínas/imunologia , SARS-CoV-2/patogenicidade , Sensibilidade e Especificidade , Imagem Individual de Molécula/métodos , Vírion/química
12.
Sci Rep ; 11(1): 20363, 2021 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-34645929

RESUMO

COVID-19 diagnostics was quickly ramped up worldwide early 2020 based on the detection of viral RNA. However, based on the scientific knowledge for pre-existing coronaviruses, it was expected that the SARS-CoV-2 RNA will be detected from symptomatic and at significant rates also from asymptomatic individuals due to persistence of non-infectious RNA. To increase the efficacy of diagnostics, surveillance, screening and pandemic control, rapid methods, such as antigen tests, are needed for decentralized testing and to assess infectiousness. A novel automated mariPOC SARS-CoV-2 test was developed for the detection of conserved structural viral nucleocapsid proteins. The test utilizes sophisticated optical laser technology for two-photon excitation and individual detection of immunoassay solid-phase particles. We validated the new method against qRT-PCR. Sensitivity of the test was 100.0% (13/13) directly from nasopharyngeal swab specimens and 84.4% (38/45) from swab specimens in undefined transport mediums. Specificity of the test was 100.0% (201/201). The test's limit of detection was 2.7 TCID50/test. It showed no cross-reactions. Our study shows that the new test can detect infectious individuals already in 20 min with clinical sensitivity close to qRT-PCR. The mariPOC is a versatile platform for syndromic testing and for high capacity infection control screening of infectious individuals.


Assuntos
Teste Sorológico para COVID-19/métodos , COVID-19/diagnóstico , Adulto , Idoso , Antígenos Virais/análise , COVID-19/imunologia , Reações Cruzadas/imunologia , Feminino , Finlândia/epidemiologia , Humanos , Imunoensaio/métodos , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , RNA Viral/genética , Reprodutibilidade dos Testes , SARS-CoV-2/imunologia , SARS-CoV-2/patogenicidade , Sensibilidade e Especificidade
13.
Microbiol Spectr ; 9(2): e0020521, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34643409

RESUMO

The extraordinary global demand for reagents and diagnostic instruments needed for timely detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly affected their availability. In order to meet diagnostic needs, it has been necessary to develop new diagnostic procedures. To date, molecular diagnostic tools have represented the gold standard for diagnosis of SARS-CoV-2 infection, and thus an alternative and real-time PCR system was required. To this aim, a molecular rapid test which works with direct real-time RT-PCR may be a relevant aid. In the present work, the accuracy, sensitivity, and specificity of the bKIT Virus Finder COVID-19 rapid molecular test by Hyris Ltd. was evaluated. Moreover, the influence of a different swab storage medium composition was examined relative to that of a routinely used comparator assay. The Hyris Ltd. assay showed an overall agreement of 100% with the comparator based on a panel consisting of 74 retrospective positive nasopharyngeal swabs (NPSs), collected either in universal transport medium (UTM) or using ESwab. No false-positive result was achieved on samples that previously tested negative. Cross-reactivity screening on microorganisms that commonly colonize the human upper respiratory tract was not detected, excluding the risk of false-positive results. Simultaneously, drugs frequently administered to cure respiratory diseases did not interfere with the analytical performance of the assay. Our results showed that the Hyris Ltd. bKIT Virus Finder COVID-19 is a reliable assay for rapid qualitative detection of SARS-CoV-2, providing the advantage of less complex and unambiguous interpretation of results. Indeed, skilled technicians are not required, and thus the Hyris system is suitable as a rapid and easy system for SARS-CoV-2 diagnosis. IMPORTANCE In order to overcome the increased demand for diagnostic tools for the timely detection of SARS-CoV-2 infection, we tested the bKIT Virus Finder COVID-19 molecular rapid test by Hyris Ltd. The new system was confirmed as a reliable assay for rapid SARS-CoV-2 detection, since sensitivity and specificity parameters were fully satisfied. Moreover, the bKIT Virus Finder COVID-19 provides the advantage of easy results interpretation, since skilled technicians are not required, and thus the Hyris system is a valuable SARS-CoV-2 rapid diagnosis system.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Humanos , Limite de Detecção , Nasofaringe/virologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2/genética , Manejo de Espécimes
14.
Microbiol Spectr ; 9(2): e0108921, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34643445

RESUMO

Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.


Assuntos
Teste de Ácido Nucleico para COVID-19/economia , COVID-19/diagnóstico , Análise Custo-Benefício , Programas de Rastreamento/economia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/economia , Saliva/virologia , COVID-19/prevenção & controle , Proteínas do Nucleocapsídeo de Coronavírus/genética , Humanos , Illinois , Limite de Detecção , Programas de Rastreamento/métodos , Nasofaringe/virologia , Fosfoproteínas/genética , SARS-CoV-2/isolamento & purificação , Universidades , Carga Viral/métodos
15.
Microbiol Spectr ; 9(2): e0084621, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34668736

RESUMO

Isothermal amplification-based tests have been introduced as rapid, low-cost, and simple alternatives to real-time reverse transcriptase PCR (RT-PCR) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. The clinical performance of two isothermal amplification-based tests (Atila Biosystems iAMP coronavirus disease of 2019 [COVID-19] detection test and OptiGene COVID-19 direct plus RT-loop-mediated isothermal amplification [LAMP] test) was compared with that of clinical RT-PCR assays using different sampling strategies. A total of 1,378 participants were tested across 4 study sites. Compared with standard of care RT-PCR testing, the overall sensitivity and specificity of the Atila iAMP test for detection of SARS-CoV-2 were 76.2% and 94.9%, respectively, and increased to 88.8% and 89.5%, respectively, after exclusion of an outlier study site. Sensitivity varied based on the anatomic site from which the sample was collected. Sensitivity for nasopharyngeal sampling was 65.4% (range across study sites, 52.8% to 79.8%), for midturbinate was 88.2%, for saliva was 55.1% (range across study sites, 42.9% to 77.8%), and for anterior nares was 66.7% (range across study sites, 63.6% to 76.5%). The specificity for these anatomic collection sites ranged from 96.7% to 100%. Sensitivity improved in symptomatic patients (overall, 82.7%) and those with a higher viral load (overall, 92.4% for cycle threshold [CT] of ≤25). Sensitivity and specificity of the OptiGene direct plus RT-LAMP test, which was conducted at a single study site, were 25.5% and 100%, respectively. The Atila iAMP COVID test with midturbinate sampling is a rapid, low-cost assay for detecting SARS-CoV-2, especially in symptomatic patients and those with a high viral load, and could be used to reduce the risk of SARS-CoV-2 transmission in clinical settings. Variation of performance between study sites highlights the need for site-specific clinical validation of these assays before clinical adoption. IMPORTANCE Numerous SARS-CoV-2 detection assays have been developed and introduced into the market under emergency use authorizations (EUAs). EUAs are granted primarily based on small studies of analytic sensitivity and specificity with limited clinical validations. A thorough clinical performance evaluation of SARS-CoV-2 assays is important to understand the strengths, limitations, and specific applications of these assays. In this first large-scale multicentric study, we evaluated the clinical performance and operational characteristics of two isothermal amplification-based SARS-CoV-2 tests, namely, (i) iAMP COVID-19 detection test (Atila BioSystems, USA) and (ii) COVID-19 direct plus RT-LAMP test (OptiGene Ltd., UK), compared with those of clinical RT-PCR tests using different sampling strategies (i.e., nasopharyngeal, self-sampled anterior nares, self-sampled midturbinate, and saliva). An important specific use for these isothermal amplification-based, rapid, low-cost, and easy-to-perform SARS-CoV-2 assays is to allow for a safer return to preventive clinical encounters, such as cancer screening, particularly in low- and middle-income countries that have low SARS-CoV-2 vaccination rates.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Amplificação de Ácido Nucleico/métodos , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Humanos , Limite de Detecção , Programas de Rastreamento , Nasofaringe/virologia , Sistemas Automatizados de Assistência Junto ao Leito , RNA Viral/análise , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Manejo de Espécimes , Carga Viral
16.
Microbiol Spectr ; 9(2): e0073621, 2021 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-34668741

RESUMO

The supply of testing equipment is vital in controlling the spread of SARS-CoV-2. We compared the diagnostic efficacy and tolerability of molded plastic (FinSwab; Valukumpu, Finland) versus flocked nylon (FLOQSwab; Copan, Italy) nasopharyngeal swabs in a clinical setting. Adults (n = 112) with suspected symptomatic COVID-19 infection underwent nasopharyngeal sampling with FinSwab and FLOQSwab from the same nostril at a drive-in coronavirus testing station. In a subset of 36 patients the samples were collected in a randomized order to evaluate the discomfort associated with sampling. SARS-CoV-2 and 16 other respiratory viruses, as well as human ß-actin mRNA were analyzed by using reverse transcriptase PCR (RT-PCR) assays. Among the 112 patients (mean age, 38 [standard deviation (SD), 14] years) ß-actin mRNA was found in all samples. There was no difference in the ß-actin mRNA cycle threshold (CT) values between FinSwab (mean, 22.3; SD, 3.61) and FLOQSwab (mean, 22.1; SD, 3.50; P = 0.46) swabs. There were 31 virus-positive cases (26 rhinovirus, 4 SARS-CoV-2, and 1 coronavirus-OC43), 24 of which were positive in both swabs; 3 rhinovirus positives were only found in the FinSwab, and similarly 4 rhinovirus positives were only found in the FLOQSwab. Rhinovirus CT values were similar between swab types. Of the 36 patients, 22 (61%) tolerated the sampling with the FinSwab better than with the FLOQSwab (P = 0.065). The molded plastic nasopharyngeal swab (FinSwab) was comparable to the standard flocked swab in terms of efficacy for respiratory virus detection and tolerability of sampling. IMPORTANCE We demonstrate that a molded plastic swab is a valid alternative to conventional brush-like swabs in collection of a nasopharyngeal sample for virus diagnostics.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , Nasofaringe/virologia , SARS-CoV-2/isolamento & purificação , Manejo de Espécimes/instrumentação , Actinas/genética , Adolescente , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Plásticos , RNA Mensageiro/genética , Infecções Respiratórias/diagnóstico , Rhinovirus/isolamento & purificação , Manejo de Espécimes/métodos , Adulto Jovem
17.
Cell Rep ; 37(3): 109838, 2021 10 19.
Artigo em Inglês | MEDLINE | ID: mdl-34648735

RESUMO

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads, variants with enhanced virulence and transmissibility have emerged. Although in vitro systems allow rapid characterization, they do not fully recapitulate the dynamic interaction of virions and neutralizing antibodies in the airway. Here, we demonstrate that the N501Y variant permits respiratory infection in unmodified mice. We utilize N501Y to survey in vivo pseudovirus infection dynamics and susceptibility to reinfection with the L452R (Los Angeles), K417N + E484K (South Africa), and L452R + K417N + E484Q (India) variants. Human coronavirus disease 2019 (COVID-19)+ or vaccinated antibody isotypes, titers, variant receptor binding domain (RBD) binding, and neutralization potential are studied, revealing numerous significant correlations. Immune escape of the K417N + E484K variant is observed because infection can be appreciated in the nasopharynx, but not lungs, of mice transferred with low-antibody-tier plasma. Conversely, near-complete protection is observed in animals receiving high-antibody-tier plasma, a phenomenon that can only be appreciated in vivo.


Assuntos
Anticorpos Antivirais/imunologia , COVID-19/imunologia , COVID-19/terapia , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Animais , Anticorpos Neutralizantes/imunologia , Linhagem Celular , Cricetinae , Variação Genética , Células HEK293 , Humanos , Sistema Imunitário , Imunização Passiva/métodos , Técnicas In Vitro , Camundongos , Mutação , Nasofaringe/virologia , Ligação Proteica , Proteínas Recombinantes/metabolismo , Glicoproteína da Espícula de Coronavírus/genética
18.
Virol J ; 18(1): 202, 2021 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-34627307

RESUMO

BACKGROUND: The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. METHODS: This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children's Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. RESULTS: A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001). CONCLUSIONS: Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.


Assuntos
Antibiose , COVID-19/epidemiologia , Doenças Respiratórias/epidemiologia , SARS-CoV-2/isolamento & purificação , Adenovírus Humanos/genética , Adenovírus Humanos/isolamento & purificação , Adolescente , COVID-19/virologia , Criança , Criança Hospitalizada , Pré-Escolar , China , Enterovirus/genética , Enterovirus/isolamento & purificação , Feminino , Humanos , Lactente , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Masculino , Metapneumovirus/genética , Metapneumovirus/isolamento & purificação , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/isolamento & purificação , Nasofaringe/microbiologia , Nasofaringe/virologia , Prevalência , Vírus Sinciciais Respiratórios/genética , Vírus Sinciciais Respiratórios/isolamento & purificação , Doenças Respiratórias/microbiologia , Doenças Respiratórias/virologia , Respirovirus/genética , Respirovirus/isolamento & purificação , SARS-CoV-2/genética
19.
Emerg Microbes Infect ; 10(1): 2090-2097, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34689717

RESUMO

Since December 2019, coronavirus disease 2019 (COVID-19) caused by SARS coronavirus 2 (SARS-CoV-2) has spread and threatens public health worldwide. The recurrence of SARS-CoV-2 RNA detection in patients after discharge from hospital signals a risk of transmission from such patients to the community and challenges the current discharge criteria of COVID-19 patients. A wide range of clinical specimens has been used to detect SARS-CoV-2. However, to date, a consensus has not been reached regarding the most appropriate specimens to use for viral RNA detection in assessing COVID-19 patients for discharge. An anal swab sample was proposed as the standard because of prolonged viral detection. In this retrospective longitudinal study of viral RNA detection in 60 confirmed COVID-19 patients, we used saliva, oropharyngeal/nasopharyngeal swab (O/N swab) and anal swab procedures from admission to discharge. The conversion times of saliva and anal swab were longer than that of O/N swab. The conversion time of hyper sensitive-CRP was the shortest and correlated with that of CT scanning and viral detection. Some patients were found to be RNA-positive in saliva while RNA-negative in anal swab while the reverse was true in some other patients, which indicated that false negatives were inevitable if only the anal swab is used for evaluating suitability for discharge. These results indicated that double-checking for viral RNA using multiple and diverse specimens was essential, and saliva could be a candidate to supplement anal swabs to reduce false-negative results and facilitate pandemic control.


Assuntos
Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , SARS-CoV-2/isolamento & purificação , Saliva/virologia , Adulto , Canal Anal/virologia , Reações Falso-Negativas , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Orofaringe/virologia , Alta do Paciente , RNA Viral/análise , Estudos Retrospectivos , Adulto Jovem
20.
Sci Rep ; 11(1): 21126, 2021 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-34702867

RESUMO

Rapid identification of SARS-CoV-2-infected individuals is a cornerstone for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swabs. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis. We conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV) designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR, to saliva RT-PCR and to nasopharyngeal antigen testing. Overall, 117 of the 1718 participants (7%) tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% and 97%, respectively. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p = 0.028). Considering six alternate criteria for reference tests, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%. The detection of SARS-CoV-2 in crude saliva samples with an RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration number: NCT04578509.


Assuntos
Assistência Ambulatorial/métodos , Teste de Ácido Nucleico para COVID-19/métodos , COVID-19/diagnóstico , COVID-19/metabolismo , SARS-CoV-2 , Saliva/metabolismo , Adulto , Testes Diagnósticos de Rotina , Reações Falso-Negativas , Reações Falso-Positivas , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Medicina Molecular , Nasofaringe/virologia , Técnicas de Amplificação de Ácido Nucleico , Sistemas Automatizados de Assistência Junto ao Leito , Testes Imediatos , Estudos Prospectivos , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
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