For the first time, Vietnamese scientists have successfully developed a technological process used for sequencing the SARS-CoV-2 virus genome through PacBio long-read genome sequencing technologies.
By utilising this technology, local scientists will be able to sequence the genomes of emerging disease-causing viruses in a rapid and accurate manner without the need to use reference genomes.
The technological process of sequencing the SARS-CoV-2 virus genome by using the modern sequencing machine PacBio is the result of a scientific project assigned by the Vietnam Academy of Science and Technology (VAST) to the Institute of Biotechnology for implementation. This is being done for the purpose of supporting the country’s handling of the novel coronavirus (COVID-19) pandemic.
Prof. Dr. Truong Nam Hai, project leader, stated that the Institute of Biotechnology has collaborated alongside the Pasteur Institute in Ho Chi Minh City and the National Institute of Hygiene and Epidemiology (NIHE) to develop this technical process through six steps. Including, culture and isolation of viral RNA and synthesis of double-stranded DNA from viral RNA. These two steps are carried out at the Pasteur Institute in Ho Chi Minh City and NIHE in a clean room of class III biosafety.
This is in addition to preparing the DNA library for gene sequencing, sequencing the whole genome of the SARS-CoV-2 virus, de novo assembly of the viral genome, and annotation and analysis of viral genomes. These steps can performed at the Institute of Biotechnology in roughly 48 hours.
Furthermore, Prof. Hai added that to sequence the SARS-CoV-2 virus in Vietnam, domestic units must use short-read sequencing technology, then assemble and reference the previous genome. This technology can take up to four days to read the complete genome and it is possible that errors occur in the reading process.
This process can sequence the entire genomes of four strains of the SARS-CoV-2 virus, with a length of over 29,500 nucleotides/genome. The genome assembly results indicate no reading errors or blanks and boasts an accuracy of 99.99%, Prof. Hai emphasised.
Through the development and mastering of PacBio's long-read genome sequencing technology for the SARS-CoV-2 virus, Vietnamese scientists believe that it has opened up the possibility of fast and accurate viral genome sequencing without the need to rely on international references for genetic sequencing.
This therefore enables local scientists to sequence new viral pathogens in the future without requiring a reference genome.
Genome sequencing data can contribute to identifying the viral origin and sources of infection, known as F0, in outbreaks. This serves as a scientific basis and important information in the development of strategies and plans for effective prevention and control methods against the spread of the virus to the community.
Assoc. Prof. Dr. Ha Quy Quynh, head of the Technology Application Department under the VAST, said, "The successful research on the technological process of decoding the SARS-CoV-2 virus gene has contributed to building a proper treatment regimen for coping with the pandemic. Specifically, gene sequencing along with tracing allows us to determine the source of the virus's spread stemming from F0s, from which we can zone off affected areas and isolate the number of people involved. This is also a scientific basis for deploying optimal treatment regimens.”
With the mastery of the existing technological process, capacity, and conditions, the VAST is ready to co-operate alongside other health units in sequencing the SARS-CoV-2 virus genome on a large scale in urgent cases, in order to effectively boost local COVID-19 prevention and control efforts.
The National Hospital for Tropical Diseases has discovered two new variants of SARS-CoV-2 after gene sequencing of patient samples.