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./.

Ancient corona virus illustration, 25,000 years ago. The current COVID-19 pandemic has claimed the lives of more than 3 million people and shows how vulnerable people are to the genetically modified corona virus. However, this threat seems to have occurred since the early days when humans had to fight these dangerous viruses. “There are always viruses that infect humans,” said senior study author David Enard, associate professor of ecology and evolution at the University of Arizona, USA. Viruses are actually one of the main drivers of natural selection in the human genome. That’s because genes that increase the chances of the pathogen’s survival are more likely to be passed on to new generations. ” Using modern tools, researchers can detect traces of these ancient pathogens by precisely identifying how they promote natural selection in today’s human DNA. Accordingly, this information can provide valuable insight to help predict future pandemics. Enard said: “Almost always is when things that happened in the past are more likely to happen in the future.” Using information available in public databases, Enard and his team analyzed the genomes of 2,504 people across 26 different human populations around the world. When corona viruses get inside human cells, they attack the cell’s machinery to replicate. This means that the viral success depends on its interaction with hundreds of different human proteins. Researchers magnified a set of 420 human proteins known to interact with the corona virus, 332 of which interact with SARS-CoV-2, the virus that causes COVID-19. Most of these proteins help viruses multiply inside cells, but some help cells fight viruses. The genes that encode those proteins mutate continuously and randomly, but if the mutation gives the gene an advantage, such as a better resistance to the virus – then the gene has a chance to be passed on. next or selected higher. Indeed, the researchers found that, in people of East Asian descent, certain genes interacting with the corona virus were selected. In other words, over time certain variations show up more often than expected. This set of mutations may have helped the ancestors of the human population in this region become more ancient antiviral by altering the amount of protein produced by the cell. The genetic variations encoding 42 of the 420 proteins they analyzed began to increase in frequency about 25,000 years ago, the researchers found. The spread of beneficial variants continued until about 5,000 years ago. This suggests that the ancient virus continued to threaten these populations for a long time. Viruses cause pressure to adapt “Viruses exert some of the strongest selective pressures on humans to adapt, and corona viruses have probably been around since,” said Joel Wertheim, associate professor at the Faculty of Medicine at the University of California, San Diego. long before man existed. However, it is difficult to say whether the virus that caused this evolution is the corona virus, but it seems to be a plausible theory. David Enard agrees that the ancient pathogen that harmed our ancestors may not have been the corona virus; instead, it is possible that another virus that has happened to interact with human cells in the same way that corona viruses do. Another group of researchers recently discovered that sarbecovirus, a family of the corona virus that includes SARS-CoV-2, first evolved 23,500 years ago, at the same time as variations in the genes that encode the proteins related to the corona virus have appeared for the first time in humans. Findings of the sarbecovirus virus were also published in bioRxiv on February 9 and have yet to be peer reviewed. While these findings are compelling, they do not change our understanding of which populations are more likely to survive SARS-CoV-2 infection. Although, there is no evidence that adaptation of this ancient gene protects modern humans from SARS-CoV-2. Enard and his team now hope to work with virologists to understand how this adaptation helped ancient humans survive exposure to this protozoan strain of the corona virus. The team also hopes that such ancient genomic studies could eventually be used as an “early warning system” for future pandemics. David Enard adds, although we clearly see the impact of this ancient virus on human ancestors, future generations will not be able to see traces of SARS-CoV-2 in the genome. our. Thanks to vaccination, there is no time for the virus to promote evolutionary adaptation.

While countries in turn closed their borders, scientists have broken their own borders, creating a global collaboration unlike anything that has happened in history. Never before have so many experts in many countries focused on a single topic and with such urgency, the researchers said. Nearly all other studies have to be halted. Within a few months, all of the global science was almost “COVIDed”. Photo: LG In a survey of 2,500 researchers in the US, Canada and Europe, Kyle Myers from Harvard and his team found that 32% turned their focus to pandemic. Neuroscientists studying olfaction are beginning to understand why patients with COVID-19 tend to lose their sense of smell. Physicists set out to create predictive models that inform policy-makers. Michael DL Johnson at the University of Arizona often studies copper’s toxic effects on bacteria. But knowing that nCoV existed on the copper surface for less time than other materials, he turned to investigating how vulnerable the virus might be to the metal. No disease has been so scrutinized by so many combined intelligence in such a short time. As of February 2021, the PubMed Biomedical Library listed more than 74,000 nCoV-related scientific articles – more than double those of articles on polio, measles, cholera, dengue, or other diseases. another has inflicted on mankind for centuries. Only 9,700 articles related to Ebola have been published since it was discovered in 1976. By September 2020, the prestigious New England Journal of Medicine received 30,000 nCoV-related articles – many 16,000 more than all of 2019. “All that difference is COVID-19,” said Eric Rubin, editor-in-chief of the New England Journal of Medicine. “This is an unprecedented shift in scientific priorities,” said Francis Collins, director of the US National Institutes of Health. In addition, online archives are readily available to provide research data and evidence before periodic scientific journals. Scientists identify and share dozens of viral genome sequences. More than 200 clinical trials have been launched, bringing together hospitals, laboratories and hundreds of thousands of volunteers globally. Speaking in The New York Times, Dr. Francesco Perrone, who leads a clinical trial of nCoV in Italy, said: “I have never heard genuine and excellent scientists talk about nationality. mine, your country. My language, your language. My geographic location, your geographic location. This is really far from true senior scientists. Photo: LG The New York Times revealed that one morning, University of Pittsburgh scientists discovered a weasel after exposure to COVID-19 particles developed a high fever. This is a potential step forward for vaccine testing in animals. Under normal circumstances, they would begin to review the research results with an article in an academic journal. But Professor Paul Duprex, the university’s lead virologist, shared the results with scientists around the world in just two hours, instead of spending months on an article. . A small measure of openness can be found on the servers of medRxiv and bioRxiv, two online archives that share academic data before it is published in journals. The archives are filled with thousands of coronavirus studies around the globe. Chinese researchers have contributed a considerable part to the nCoV research in this treasure. A Chinese lab announced the original virus genome in January, providing the basis for nCoV tests worldwide. Thanks to this initial genetic data, the world’s leading research institutions have based and supplemented the evidence, thereby successfully testing vaccine products with a preventive effect of up to 90% – 95%, in a time of unprecedented speed in history. By November, more than 197,000 nCoV genomes had been sequenced. Lauren Gardner, an engineering professor at Johns Hopkins University who has studied dengue and Zika, knows that the new diseases will come with a scarcity of real-time data. So she and her students created a global online map to count all COVID-19 cases and deaths. After one night’s work, they launched it on January 22. / 2020. Since then, the dashboard has been accessed daily by governments, public health agencies, the media and anxious global citizens. One of the foe-to-friend partnerships mentioned is a joint production cooperation agreement between US pharmaceutical firm J&J’s COVID-19 vaccine and leading rival Merck in March 2021. Emphasizing that the US is in a state of “national emergency” and it is time to act “drastically and boldly”, the two rivals have begun to speed up the production of vaccines, aiming to supply the country. 200 million doses in 2021, bringing America to community immunity. Photo: LG From Asia to Europe, Africa to the Americas, despite the differences in politics, culture, ethnicity, language … scientists share, cooperate, seek all vaccine solutions and remedy against viruses. Even though large, proprietary research may lead to sponsorship, promotion and reputation, scientists have left behind secret ways of working, hoarding data from competitors, to together find the light at the end of the tunnel to save all of humanity. These efforts have paid off. New diagnostic tests can detect the virus within minutes. Huge open datasets on the viral genome and cases of COVID-19 give the most detailed picture of the evolution of a disease that has never appeared in history. Along with the new discoveries revolving around, humankind is prepared with an abundance of scientific resources to be ready for the face of future pandemic. In particular, if no one dared to say anything for sure in March 2020, the positive results of a series of vaccines plus successful antiviral drug antibodies would have brought people to life. closer to the prospect of ending the pandemic. A series of countries launch a campaign to vaccinate hundreds of millions of people by 2021, with the aim of achieving the earliest community immunity, to bring the entire country back to normal as before. Borders will reopen, and laboratories and research facilities around the globe will revive again, and continue to seek solutions that will push humanity toward the future. That is the unchanging mission of science, in any historical moment.

Axolotl is a species of salamander being hunted by the world science world. The reason is its unique feature: Many lost parts can be reproduced.

According to the New York TimesAxolotl also has an unusual feature compared to other amphibians that do not undergo molting, change shape. They have a pale pink, yellow or gray, black appearance; Spotted body with a smiling face.

Today, this animal is in danger of being threatened by the environment and by human hunting. Axolotl survives only in the canals of Lake Xochimilco, the southernmost tip of Mexico.

The mystery of the genome of a self-regenerating animal

Researcher Randal Randal Voss, University of Kentucky, USA, said: “It is difficult to find things that they cannot replicate: From limbs, tail, spinal cord, eyes, even the retina in some “We have also seen the process of regenerating half of their brains.”

Thanks to this feature, the genome of Axolotl has become something of interest to the scientific community. Recently, in an upcoming article to be published in the Proceedings of the National Academy of Sciences (PNAS) on April 13, geneticists have a clearer view of the salamanders genome. This is on the chromosome scale, in the folded form. The study was chaired by the authors at the Vienna Center for Biology, BioCenter Institute for Molecular Pathology, Austria.

The study looks at how the genome of Axolotl folds inside at the molecular level and the position of the DNA sequences that regulate the genes involved in the regeneration and healing of cells. When fully stretched, each human DNA strand is longer than 1.8 m. However, Axolotl’s DNA strand is more than 9.1 m long.

A wild Axolotl in a conservation laboratory in Mexico in 2014. Photo: AFP.

“This work has arranged the DNA fragments in the Axolotl genome in the right order, as if it were on a chromosome. This is very important because in all vertebrates, genes are turned on and off with a controlled sequence located quite far from them, ”says biochemist Elly Tanaka, Vienna Institute of Molecular Pathology, BioCenter. about Axolotl but not participating in this project, reviews.

She also said that the study of the authors at the BioCenter Molecular Pathology Institute is very important because it will answer the question of whether the regeneration mechanism in Axolotl can be activated in humans.

After regenerating the entire gene in the folded form of Axolotl, the authors expect to simulate it in 3D in the future.

Two mysterious genes of Axolotl

According to Professor, Dr. Parker Flowers, Craig Crews Laboratory, Yale University, USA, Axolotl regenerates, self-healing most organs and organs after any injury. Therefore, it is difficult to have any injuries to kill this salamander.

If scientists find the genetic basis for the regenerative ability of Axolotl, they may discover something unprecedented. It is a way of restoring damaged tissues in humans.

But that job is not easy. Because the characteristics of the species Axolotl are not like humans. They have a larger genome than any other animal that humans have ever sequenced. This genome is even 10 times larger than the entire human genome.

At the end of January 2020, Professor Parker and his colleagues in the magazine post eLife revealed they have found the key to these problems. The authors found a way to disrupt the complex genome of the salamander Axolotl and identify at least two genes involved in post-traumatic body regeneration.

According to the Science Daily, the advent of next-generation gene-editing and sequencing technologies has allowed researchers to list hundreds of gene candidates that can reproduce the extremities. However, the giant size of the Axolotl genome produces repetitive DNA fragments, making it difficult to dissect and analyze them.

Researcher Lucas Sanor, co-author of the Craig Crews lab project, used multi-step gene editing to record baseline markers, tracking 25 genes believed to be involved in the regeneration process. Genus in Axolotl. Thanks to that, they identified two genes in blastema dividing cells responsible for regenerating part of their tail when injured or severed.

But that’s not all. Professor Parker emphasized that Axolotl’s body still has many similar genes. And humans have similar DNA with Axolotl so scientists can discover how to activate tissue, cells speed up wound repair, regenerate lost parts.

Axolotl salamander has a pale pink, yellow or gray, black appearance, and a smiling face. Photo: Getty Images.

Decoding the entire gene of Axolotl for the first time

Before the study of Professor Parker Flowers and colleagues, at the end of November 2018, the group of authors at the University of Kentucky, USA, published the most complete simulation of Axolotl’s DNA. Research published in the journal Genome Research, is considered to pave the way for transformations in human regenerative medicine.

Many animals are able to perform some degree of regeneration and self-healing. However, Axolotl is the only species that is nearly limitless in terms of this ability. Associate Professor, Dr. Jeramiah Smith, University of Kentucky and colleagues decided to find answers about the healing superpower of Axolotl through sequencing all genes.

Based on previous research, the authors have mapped more than 100,000 pieces of DNA onto chromosomes, the genetic makeup in the nucleus of each cell. The Axolotl genome is the largest product assembled at this level.

The authors used a design mapping method, which relies on the fact that the strands of DNA are physically close together on one chromosome and tend to move together. To determine the specific DNA of Axolotl, they grafted Axolotl with the tiger salamander – a close relative. They were then mated back to generation F1 with purebred Axolotl.

The process of regeneration of the extremities of Axolotl salamander. Photo: eLife.

Tracking genotypes on 48 out of all F2, they were able to deduce which DNA sequences belong to the Axolots and where they are located in the 14 chromosomes of amphibians. During the study, the authors identified a genetic mutation that causes heart defects in Axolotl.

“Just a few years ago, no one thought it was possible to decode genomes with more than 30 GB capacity. Now, we have many methods to approach and open up the ability to decode large genomic animals more often, “says biological researcher Jeramiah Smith.

The team also hopes that understanding the axolotl’s post-sequencing genome will help in future medicine. “Now we can go into the genome sequence, find out what makes this salamander strange. Hopefully one day, we can make the collected information useful for human therapy, the potentials that may not be fully exploited of each part of the body ”, Mr. Voss identify.