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Objective:To establish and evaluate a rapid nucleic acid detection method for SARS-CoV-2 based on COYOTE ? Flash20 real-time fluorescent quantitative PCR instrument. Methods:A rapid reaction system was constructed by using specific primer and probe sets targeting ORF1ab and N gene of SARS-CoV-2, and the sensitivity and specificity of the system were verified. At the same time, 108 clinical samples of COVID-19 were used to evaluate the application of this method.Results:The detection method did not require nucleic acid extraction, and the manual operation time was only one minute. After the sample was sent to the system, the test could be completed in 30 minutes. The detection limit of this method was 4×10 2 copies/ml. It had no cross-reactivity with other human coronaviruses (including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV and MERS-CoV) and other respiratory viruses. The evaluation of clinical sample application showed that the total coincidence rate with the conventional RT-qPCR which required nucleic acid extraction was 98.15%. Conclusions:Through the application evaluation of the rapid fluorescent quantitative PCR method of SARS-CoV-2, it was found that the method was simple, fast, specific and sensitive, and it was suitable for real-time and rapid detection needs in varieties of situations.
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Objective:To study the effects of different pre-sequencing sample processing modes on the results of whole genome sequencing with high-throughput sequencing (HTS) by taking the largest RNA virus (human coronavirus, HCoV) as the representative.Methods:Cell-cultured human coronavirus HCoV-OC43 strains were used as the representative samples and divided into different groups based on pre-sequencing processing modes as follows: untreated group, DNase and RNase treatment before nucleic acid extraction group, DNase treatment after nucleic acid extraction group, and DNase and RNase treatment before nucleic acid extraction and DNase treatment after nucleic acid extraction group. Nucleic acid samples of each group were analyzed by direct RNA sequencing (without amplification) and DNA sequencing after sequence independent single primer amplification (SISPA), respectively.Results:No significant difference in viral genome coverage rates was observed between different groups. The highest genome coverage and sequencing accuracy were obtained in DNase treatment after nucleic acid extraction group by direct RNA sequencing, and the ratio of viral reads and the sequencing depth of each locus were effectively improved by SISPA amplification.Conclusions:This study provided an optimized technical strategy for whole genome sequencing of RNA viruses such as coronavirus.
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Objective To investigate the possibility of using well-differentiated human airway epithelial cells (HAE) to isolate and identify human influenza A virus from a stale respiratory tract specimen.Methods The stale specimen used in this study was a nasopharyngeal swab specimen collected from a patient with unexplained pneumonia in Qinghai in 2010.It was positive for influenza A virus (H3N2) RNA, but negative for hemagglutination.Equal amount of the specimen was inoculated on HAE and on Madin-Darby canine kidney (MDCK) cells for virus isolation and passage.Cytopathic effects were observed daily after inoculation.Hemagglutination inhibition test was performed at every passage.Electron microscope was used to observe viral morphology.Viral genome was sequenced, followed by molecular evolutionary analysis.Results No progeny virus was isolated in MDCK cells, while a influenza A virus subtype H3N2 strain [A/Qinghai/178/2010(H3N2)] was isolated in HAE with a typical morphology and cytopathic effect of influenza A infection.The hemagglutination inhibition activity was 1∶16.Results of the molecular evolutionary analysis of viral genome showed that the influenza A virus (H3N2) strain was highly homologous to the A/Nanjing/1655/2010(H3N2) strain, which was isolated during the 2010 influenza pandemic in Nanjing.Conclusion HAE can be used for isolation and identification of virus from stale respiratory tract specimens.It is more sensitive than MDCK cells with regard to human influenza virus isolation.
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In this study, we evaluated the difference ot biological characteristics in the MERS-CoV infected mice model in prior to transduction with different dosage of human DPP4. Firstly, we transduced different dosage of DPP4 (high or low) into mice, and then challenged them with MERS-CoV in order to establish the model. After establishment of mice model, we observed the clinical signs of disease, virus replication, immunopathogenesis and antibody response. The results indicated that the infected mice showed typical pneumonia, virus replication, histological lesions, and neutralizing antibody production. Moreover, the high dosage group was superior to the low dosage group. Fourteen days after infection, the specific antibody to virus structural protein and neutralizing antibody were analyzed, the high dosage group induced higher level antibody. In summary, the MERS-CoV infected mice model were established prior transduction with DPP4, and the level of DPP4 influenced the clinical signs of disease, virus replication and antibody response in this model.
Subject(s)
Animals , Female , Humans , Mice , Coronavirus Infections , Genetics , Pathology , Virology , Dipeptidyl Peptidase 4 , Genetics , Metabolism , Disease Models, Animal , Mice, Inbred BALB C , Middle East Respiratory Syndrome Coronavirus , Genetics , PhysiologyABSTRACT
<p><b>OBJECTIVE</b>To develop an one-tube multiplex RT-PCR assay for simultaneous detection of six human coronaviruses (HCoVs).</p><p><b>METHODS</b>Genbank sequences of six human coronaviruses, including HCoV-NL63, HCoV-229E, SARS-CoV, HCoV-OC43, MERS-CoV, and HCoV-HKU1, were included as reference sequences. Primers were designed based on multiple alignment of reference sequences, targeting the conserved regions of each species of HcoV. Virus strains and nucleic acid preserved in our lab were used as template in developing this automatic-electrophoresis-based one-tube multiplex RT-PCR assay. Detection limits and reproducibility were also evaluated with these templates. Samples with infection of other respiratory viruses preserved in our lab were used to evaluate specificity of this assay. Finally, we tested this assay with 140 clinical samples that were validated by real-time PCR in parallel.</p><p><b>RESULTS</b>This automatic-electrophoresis-based multiplex RT-PCR assay was able to detect six human coronaviruses simultaneously. All positive samples in this study were detected with at least one specific fragment of anticipated length (195, 304, 332, 378, 415, 442 bp) . No fragment was detected in negative controls. Detection limits of 1.0×10(1-1.0)×10(2) copies/µl were achieved in tests of single virus. No cross reaction was observed with other respiratory viruses. This multiplex RT-PCR assay showed the same sensitivity and specificity to that of individual real-time RT-PCR validated with clinical samples. Both methods detected 28 positive samples (20%) .</p><p><b>CONCLUSIONS</b>Six HCoVs can be detected in one tube by this novel multiplex RT-PCR assay with high sensitivity and specificity.</p>