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Culturing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnosis and genome sequencing

ABSTRACT: Culturing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnosis and genome sequencing

PROVIDER: PRJNA784292 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17055661.fastq.gz	Fastqsanger.gz
	SRR17055662_1.fastq.gz	Fastqsanger.gz
	SRR17055662_2.fastq.gz	Fastqsanger.gz
	SRR17055663_1.fastq.gz	Fastqsanger.gz
	SRR17055663_2.fastq.gz	Fastqsanger.gz

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Culturing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for diagnosis and genome sequencing

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Culturing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Diagnosis and Genome Sequencing.

Project description:ObjectiveThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid detection "re-positive" phenomenon is encountered clinically. The accuracy of a viral nucleic acid test is crucial to prevent reintroduction of the virus into the community. This study evaluated the effect of virus culturing on increasing the sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) detection and viral genomic sequencing.MethodsA series of tenfold dilutions of a SARS-CoV-2 viral stock were conducted and cultured for either 24 or 48 hours. The viral load of cultured samples was determined by RT-PCR. The cultured and non-cultured samples of 1x 50% tissue culture infectious dose (TCID50) were sequenced using metagenomic next-generation sequencing. The depth and coverage of SARS-CoV-2 genome were measured.ResultsThe lowest viral load detectable in a sample with RT-PCR was 0.01 TCID50. After a 24-h culture, the viral ORF 1ab and N-gene cycle threshold (CT) values were reduced by 4.4 points and 1 point, respectively. One TCID50 viral load of post 24-h culture revealed the sequence depth reached an average of 752 reads, compared with 0.15 in the nonculture; furthermore, the coverage was 99.99% while 6.42% in the nonculture.ConclusionThese results indicate that virus culturing can significantly increase the viral load, which can increase the certainty of true-positive detection of the viral nucleic acids, and improve the quality of virus genomic sequencing.

| S-EPMC9214156 | biostudies-literature

Severe acute respiratory syndrome coronavirus 2 strain:SARS-CoV-2

Project description:Severe acute respiratory syndrome coronavirus 2 strain:SARS-CoV-2 Raw sequence reads

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Severe acute respiratory syndrome coronavirus 2 strain:SARS-CoV2

Project description:Severe acute respiratory syndrome coronavirus 2 strain:SARS-CoV2 Raw sequence reads

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Cell host-response to infection with novel human coronavirus EMC predict potential antivirals and important differences with SARS-coronavirus.

Project description:Differential expression was determined in Calu-3 cells between mock infected and infection with either Human coronavirus EMC and SARS coronavirus at different times post infection. Calu-3 2B4 cells were infected with Human Coronavirus EMC 2012 (HCoV-EMC) or mock infected. Samples were collected 0, 3, 7, 12, 18 and 24 hpi. There are 3 mock and 3 infected replicates for each time point, except for 12 hpi for which there are only 2 infected replicates (one replicate did not pass RNA quality check). There were no mock sampes at 18 hpi, and therefore infected samples at 18 hpi were compared with mocks at 24 hpi. For direct comparison with SARS-CoV infected cells, raw data from HCoV-EMC experiments were quantile normalized together with the SARS-CoV dataset (GEO Series accession number GSE33267).

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