Institute of Biotechnology and HCMC Pasteur City Institute succeed in whole-genome sequencing and de novo assembly of SARS-CoV-2 virus on a new generation PacBio SEQUEL

21/07/2020
The COVID-19 pandemic, an acute respiratory infection caused by a new strain of coronavirus (SARS-CoV-2), has killed hundreds of thousands of people worldwide. To minimize the harmful effects of this disease, scientists have conducted many studies, such as creating a test kit to detect viruses in patient samples, research on vaccine production and preventive and treatment drugs, sequence the entire genome of viruses from strains spreading in many countries around the world and identify their variants.

At the request of reality, the Vietnam Academy of Science and Technology has assigned institutes to preside over a number of urgent tasks, including the task of sequencing the entire genome of the SARS-CoV-2 virus, hosted by the Institute of Biotechnology. The Institute of Biotechnology has actively coordinated with HCMC Pasteur Institute to carry out this task.

Principle of technology for real-time single-molecule sequencing (SMRT-sequencing) on Pacbio SEQUEL system

In the framework of cooperation, HCMC Pasteur Institute implemented steps related to the culture of virus isolated from SARS-CoV-2 infected patients on VeroE6 cells, then extracted viral RNA and synthesized cDNA double-chain from RNA. The Institute of Biotechnology used Single Molecule Real Time – SMART sequencing on the new PacBio SEQUEL sequencing device to sequence new generation PacBio SEQUEL and genome SARS-CoV-2 virus based on cDNA of virus provided by HCMC Pasteur Institute.

Results of assembly and interpretation of the genome yielded sufficient and accurate coding sequences of the SARS-CoV-2 virus. More importantly, the results were validated when compared to the reference sequences of NCBI and the sequence of SARS-CoV-2 virus strains from the HCMC Pasteur Institute, and the National Institute of Hygiene and Epidemiology registered on the World Data (GISAID) shows that the assembly sequence of the Institute of Biotechnology is highly accurate, nearly 100% similar to the reference sequences.

Results of de novo genome sequencing of SARS-CoV-2 virus by SMRT sequencing technology without reference genome showed that the Institute of Biotechnology has the ability to apply modern sequencing technology in quickly and effectively decoding new pathogens in urgent situations (both the process of setting up cDNA libraries, sequencing, assembling and annotating genes take only two days), meeting the ability to respond to an entirely new disease without waiting for support from the international community. In addition, PacBio SEQUEL device system can simultaneously solve many genomes of different virus strains (40-50 strains per chip), which is useful for investigating the path of transmission of SARS-CoV-2 virus. After this success, the Institute of Biotechnology will cooperate with HCMC Pasteur Institute and National Institute of Hygiene and Epidemiology to sequence more some strains of SARS-CoV-2 virus that are spreading in Vietnam./.

Translated by Tuyet Nhung
Link to Vietnamese version



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