For the first time, Vietnam successfully built a process for sequencing the SARS-CoV-2 virus genome

For the first time, Vietnamese scientists have successfully built a technological process for sequencing the SARS-CoV-2 virus genome using the PacBio long-segment genome sequencing technique.
With the mastery of this technology, Vietnamese scientists can sequence the genomes of new disease-causing viruses in the future quickly and accurately without the need for reference genomes.

The technological process of sequencing the SARS-CoV-2 virus genome by the new generation sequencing machine PacBio is the result of a scientific project assigned by the Vietnam Academy of Science and Technology to the Institute of Biotechnology. (biotechnology) implementation, in order to meet the needs of supporting the handling of the COVID-19 epidemic in Vietnam. Phylogenetic tree of SARS-CoV-2 strains collected in Vietnam until April 1, 2021. The NCBI reference MN908947.3 was also included as a comparison (black), while the SARS-CoV-2 genomes analyzed and provided by the Institute of Biotechnology were included in the comparison (boxed in red). Sequences are colored according to the GISAID classification. The taxonomic tree shows the evolution of SARS-CoV-2 as well as when the strains entered Vietnam one by one. Prof. Dr. Truong Nam Hai – Project leader said that the Institute of Biotechnology has collaborated with the Pasteur Institute in Ho Chi Minh City and the National Institute of Hygiene and Epidemiology (NIHE) to develop a technical process to sequence the entire SARS virus genome. CoV-2 by PacBio’s long segment sequencing technology, including 6 steps: (1) Culture and extraction of viral RNA. (2) Synthesis of double-stranded cDNA from viral RNA. These two steps were carried out at the Pasteur Institute in HCMC and NIHE in clean room conditions of class III biosafety. (3) Prepare a DNA library for gene sequencing. (4) Sequencing the whole genome of the SARS-CoV-2 virus. (5) De novo assembly of the viral genome. (6) Annotation and analysis of viral genomes. The following four steps were performed at the Institute of Biotechnology in about 48 hours. Also according to Prof. Dr. Truong Nam Hai, in Vietnam, to sequence the SARS-CoV-2 virus genome, domestic units use short-sequencing technology. Then assemble and reference the previous genome. This technology takes a long time to read the complete genome (3-4 days) and there are still errors in reading. “Some other units can sequence with next-generation equipment based on the principle of sequencing short fragments. That is, they sequence short fragments, then assemble these fragments together into long segments. To sequence a genome, and to sequence that, the units must now use the reference sequence that has been solved previously (as before, China was the country that successfully sequenced the strain in Wuhan) After solving the short segments, use the reference sequence to assemble to form the genome of the strain that we are sequencing.This is often a long process, short sequencing is often difficult to do. read the entire genome fully, so sometimes it is necessary to use an additional sequence called sanger sequencing to fully read the genome that we are interested in.Besides, this method also has other advantages. reading errors, so editing it also takes more time “- Professor Truong Nam Hai said. Prof. Dr. Truong Nam Hai also said that the project has sequenced the entire genome of four strains of SARS-CoV-2 virus, with a length of over 29500 nucleotides/genome. The results of genome assembly showed that there were no reading errors or blanks, and the sequencing results achieved 99.99% accuracy. “Currently this is the only device in Vietnam, it doesn’t have to read short paragraphs, but read long ones. Reading short paragraphs only reads 100-200 nucleotides/fragment, then assembles into a full genome. But Long segments can read thousands, tens of thousands of nucleotides/segment, and reading long fragments, when assembled to produce a genome, it is simpler and more accurate, the accuracy is equivalent to 99.99%- ie reading errors are almost nonexistent, assembly is very fast.It takes about 2 days for sequencing, assembly and analysis to complete the genome of a virus “- GS Hai said. With the construction and mastering of PacBio’s long-range genome sequencing technique for SARS-CoV-2 virus, according to scientists’ assessment, it has opened up the possibility of fast and accurate viral genome sequencing. without relying on international reference gene sequences. This allows Vietnamese scientists to sequence new viral pathogens in the future without the need for a reference genome. Genome sequencing data contributes to determining the origin of the virus and the number of sources of infection (F0) in the outbreaks, is a scientific basis and important information in the development of strategies and plans for prevention and control. effective spread of the virus in the community. Assoc. Prof. Dr. Ha Quy Quynh – Head of Technology Application and Deployment Department, Vietnam Academy of Science and Technology emphasized: “The successful study of the technological process of decoding the SARS-CoV-2 virus gene is contributed to the treatment regimen that we were able to suppress the epidemic, in particular, gene sequencing along with tracing allowed us to determine the source of the virus’s spread – the F0s, from which We have a scientific basis for us to isolate and isolate the number of people involved, and we also have a scientific basis to deploy optimal treatment regimens.” With the mastery of the existing technological process, capacity and conditions, the Vietnam Academy of Science and Technology also said that it is ready to cooperate with medical institutions in sequencing the system. genes of SARS-CoV-2 virus on a large scale in urgent cases, in order to effectively serve the prevention of COVID-19 epidemic in Vietnam./.