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./.

WHO technical team leader on Covid-19 Maria Van Kerkhove. Photo: AFP According to the new announcement, WHO will use Greek letters to refer to variants that were first detected in countries such as the UK, South Africa and India. For example, the variant in the UK is called Alpha, in South Africa it is Beta, and in India it is Delta. The full list of names has been published on the WHO website. The Government of India earlier this month criticized the naming of variant B.1.617.2 – first detected in the country last October – as “Indian variant”, despite WHO never officially called it that. “No country should be discriminated against in detecting and reporting variants,” said WHO’s Covid-19 technical team leader Maria Van Kerkhove, “we don’t want to replace scientific names.” available, but only to assist in the transmission of certain information to the general public” If more than 24 variants are officially identified, meaning the system will run out of Greek letters, WHO will announce the new designation. Ms. Van Kerkhove on May 31 also called for close monitoring of variants and sharing of scientific data to help prevent the spread. Over the weekend, Vietnamese health officials warned of a new virus variant, which is believed to be a dangerous combination of two Alpha and Delta variants. While a scientific adviser to the British Government on May 31 said that the country is in the early stages of a third wave of Covid-19 infections, partly due to the Delta variant.

Researchers wear protective gear at the Wuhan Institute of Virology. Photo: Xinhua US President Joe Biden announced last week that the US intelligence community had questioned two possible origins of the COVID-19 pandemic: “Human contact with infected animals or a laboratory incident. “. He ordered a new investigation “to bring us closer to a final conclusion”. According to Bloomberg, no matter where the investigation leads, the history of laboratory safety shows that leakage of pathogens has happened, sometimes with deadly consequences. Smallpox virus leak By the late 1970s, smallpox had been eradicated from the wild, but research on the disease continues in several laboratories around the world, including one in Birmingham (UK). where a virulent strain of smallpox virus is handled. In the summer of 1978, a medical photographer working there named Janet Parker became ill. When pustules spread on her body, the local doctor diagnosed it as a severe case of smallpox. Victim Janet Parker in the smallpox virus leak from the laboratory. It was the third leak of the smallpox virus in that decade from a UK laboratory. The British government has drastically stopped the outbreak by urgently isolating hundreds of people and vaccinating many others. Thanks to those efforts, only one other person became infected, and that was Parker’s mother. However, the female photographer experienced a painful, lonely death in quarantine, and is believed to be the last known fatal victim of smallpox. But there are other victims of the incident. At that time the press mentioned the director of the laboratory in Birmingham, a smallpox virus expert named Henry Bedson. Although there was no evidence, the media still blamed him for the incident. Quarantined at home and in despair, Bedson slit his own throat and died shortly thereafter. The British government has organized a thorough investigation into the outbreak. An investigation found Mr Bedson may not have followed adequate safety procedures and speculated that Parker contracted smallpox from a virus that leaked into the gas pipeline. Technicians at a laboratory in Rockville, Maryland (USA), where smallpox vaccine is produced. A lawsuit later dismissed this explanation, and raised the disturbing possibility that Parker herself had entered one of the workspaces without proper protection. To this day, the debate over the Parker incident remains unresolved. Anthrax spores from the lab When laboratories let pathogens leak in a secret environment, it is much harder to confirm the source of the outbreak. A case in point is the anthrax outbreak in Sverdlovsk, a rather isolated city in the former Soviet Union. In 1979, rumors of anthrax killing dozens, even thousands, began to spread to the West. Later that year, Soviet newspapers confirmed some reports, noting that more than 100 people had contracted anthrax after eating contaminated meat, and over 60 had died. It was a tragedy, but perhaps unavoidable because anthrax is readily apparent in local animal populations. However, US intelligence officials are not convinced by that. Satellite images show disinfecting truck-like objects around the city, with a significant focus of activity on a mysterious military facility known as Complex 19. CIA analysts have reported hypothesized that the Soviet Union leaked a weaponized form of anthrax. The Soviets reacted indignantly to this allegation. In 1980, Russia’s official news agency Itar Tass published a rebuttal titled “A Seed of Deception,” accusing the US of making false statements to gain geopolitical advantage. Sverdlovsk was once one of the military secret cities of the Soviet era. Then, under the administration of President Ronald Reagan, the CIA sought to better handle what happened. They asked Matthew Meselson, a distinguished geneticist at Harvard who worked on the bioweapons ban program, to directly assess the evidence. Mr. Meselson was not convinced by the US intelligence findings. In the 1980s, he rejected another theory that the Soviet Union used some kind of fungal weapon in Laos – and he initially held the same view on the anthrax case, endorsing the main explanation. information from the Soviet Union, with one important caveat: Without a thorough investigation in Sverdlovsk, it would be impossible to know for certain what happened. Essentially, Mr. Meselson supported the explanation that the meat was tainted, judging it to be “completely reasonable and consistent” based on what was known about anthrax. He also arranged meetings with Soviet scientists to add credence to this interpretation, with slides of pathology samples taken from the victims. The US intelligence community, however, remains skeptical. And in this case, the intelligence agencies, not the scientists, turned out to be right. After the breakup of the Soviet Union, Meselson and other researchers finally had access to pathological samples taken from the victims’ lungs, which showed they had died from inhaling anthrax spores. Subsequent revelations added to the picture of what happened. Turns out Complex 19 is a biological weapons facility. Here they produce anthrax spores. According to the Laboratory Director of Complex 19 at the time, a filter connected to the spore dryer was clogged. This still happens often. The military officer in charge left a message for his replacement on the next shift but did not enter the logbook as is customary. When it came to the next shift, the replacement team looked at the notebook, saw nothing, and restarted the purifier. A series of anthrax spores quickly spread throughout the vicinity. Mr. Meselson eventually pieced together all the data and published a paper in the journal Science, which combined wind data with interviews, pathological samples and other evidence to describe the outbreak. Coal killed more than 60 people. That was in 1994, 15 years after the incident. Mysterious flu virus leak In addition, there is another incident that took place in the Soviet Union that is still a mystery. In the same decade that witnessed the leaks of smallpox in Britain and anthrax in the Soviet Union, there was also an unusual strain of flu at the time, called H1N1. Laboratory virus leaks have had deadly consequences. Photo: Atlantis In 1977, an H1N1 outbreak broke out on the border between China and the Soviet Union. The epidemic eventually spread worldwide that year, causing an unusual proportion of young patients. The mortality rate from epidemics is relatively low compared to some strains of influenza. But that’s not the problem. The worrying aspect of the epidemic is that this particular strain of H1N1 has not been present since 1950, when it was superseded by other strains of influenza. The appearance of that kind of “back in time” was confusing. Some researchers speculate that the virus may have “escaped” from a laboratory in the Soviet Union or China, but both countries deny this theory. However, the matter remains a puzzle for virologists. Many theories have been born and come to explain the so-called “frozen evolution”, among which the most prominent is the hypothesis that the virus spread to humans from a laboratory, possibly testing a vaccine to neutralize the disease. swine flu. A scientist involved in the development of a vaccine. Photo: Reuters The exact origin of COVID-19 may not be known All of the above incidents occurred in the 1970s. Laboratory safety was expected to have improved since then, but that has not always been the case. After the SARS outbreak in 2003, laboratories around the world began studying the virus. Since that time, there have been no less than 6 laboratory leaks of SARS. The first occurred at the National University of Singapore, where a student contracted the virus from a sample of the virus. This was followed by an incident in Taiwan/China, where a researcher contracted the virus, possibly during the disinfection of waste products from the laboratory. After that, several leaks happened at the National Institute of Virology of China. In one incident, a researcher infected her mother with the virus, and she died of SARS. In all cases, human negligence, mainly exacerbated by inadequate safety protocols, was the cause of the pathogen leakage. History has supported the theories being put forward that the current COVID-19 pandemic may not have a natural origin, but we are not in a position to rush into judgment. When it comes to lab leaks, the investigation and review process often takes a long time, and sometimes the answers remain unsatisfactory and incomplete. In the case of the COVID pandemic, we must prepare for the possibility that the world may never know the exact origins of a pandemic that has claimed millions of lives.

People wear masks to prevent COVID-19 infection in Manila, Philippines, on March 20, 2021. Photo: THX / TTXVN The ban began to be enforced on March 20 and was initially expected to be lifted on April 21. However, the Philippines decided to extend the ban for more than a week as the Southeast Asian nation recorded an average of 10,000 new infections a day this week. Accordingly, foreigners are not allowed to enter the Philippines, except for some exceptions such as diplomats, medical staff, sailors working on cargo ships, spouses, children of Filipino citizens. together with them and a number of other humanitarian cases. According to Harry Roque, the Philippine President’s spokesman, the ban does not apply to foreign nationals with a waiver issued by the Philippine Foreign Ministry before March 22. As of April 15, the Philippines recorded a total of 904,285 cases of COVID-19, of which 15,594 were fatal. On the same day, the Government of India announced that the monuments, museums and monuments managed by the Archaeological Survey of India (ASI) will be closed until May 15, amid the number of cases. COVID-19 infection is increased in this South Asian country. In a statement, ASI stated: “Due to the raging COVID-19 epidemic, the government decided to close all protected monuments, monuments and museums, under ASI’s control, effective immediately and lasts until 5/15/2021 “. India is seeing an increase in the number of new cases of COVID-19. The Ministry of Health of this country on April 16 announced that the country had recorded 217,353 new infections in the past 24 hours. This is the 8th time that India has recorded a record high daily new cases in the past 9 days. The total number of COVID-19 cases in this country is now nearly 14.3 million, only after the US has more than 31 million cases. The total number of COVID-19 deaths in India also increased by 1,185 to 174,308.

COVID-19 vaccine for people in Ohio, USA. Photo: AFP / VNA

The country most severely affected remains the United States with 577,226 deaths out of a total of 32,075,852 cases. It was followed by India with 172,461 deaths out of 13,960,574 cases. In the past 24 hours, the country recorded an additional 184,372 cases of COVID-19 and 1,027 deaths. This is the day India has the highest number of cases ever and the highest number of deaths in 2021. April 14 is the 8th day in a row and the 9th time this month that the number of new cases has exceeded. 100,000 cases milestone in India. Third place was Brazil with 358,718 deaths out of 13,601,566 patients.

In Asia, the Philippines’ Department of Health (DOH) announced that it had recorded 8,122 new cases, bringing the total number of cases in this Southeast Asian country to 892,880 cases. According to DOH, the total number of deaths in the Philippines also increased to 15,447, 162 more than the day before. Philippine Deputy Health Minister Maria Rosario Vergeire said the rate of disease spread in this country has not decreased, the number of cases continues to increase. According to the official, the infection in the community still occurs, the outbreaks in the workplace are the main source of transmission, mainly in hospitals and closed workspaces.

On the same day, Malaysia recorded 1,889 new cases, bringing the total number of cases in this country to 365,892 cases. Malaysia also recorded eight more deaths in the past 24 hours, bringing the total number of deaths due to the disease in the country to 1,353.

Thailand is considering imposing new measures to deal with the growing number of new COVID-19 infections. On April 14, Thailand recorded the highest number of new cases of COVID-19 by day since the pandemic appeared in the country early last year. The Center for Managing the situation COVID-19 (CCSA) confirmed 1,335 new cases, bringing the total number of cases in the country to 35,910, including 97 deaths.

In Japan, leading infectious disease expert Shigeru Omi warns the country has entered the fourth wave of infection of the COVID-19 pandemic amid highly infectious variants of the SARS-CoV virus. -2 is spreading in some areas.

In the context of the complicated epidemic, the government of Matsuyama city, in the western country, decided to cancel the Tokyo Olympic torch relay ceremony. Tokyo Mayor Yuriko Koike has also pledged to effectively control the COVID-19 epidemic in the capital to ensure the upcoming Olympics take place safely. She emphasized that from now until May 11, it will be an important period to win the fight against the COVID-19 campaign before the Olympics takes place. According to statistics, Japan has recorded a total of over 513,000 infections and over 9,500 deaths due to COVID-19.

People wear masks to prevent COVID-19 epidemic in Seoul, Korea. Photo: AFP / VNA

South Korea is also facing the risk of appearing the 4th wave of infection when the number of new cases has exceeded 700 cases / day. Statistics of the Korea Agency for Disease Control and Prevention (KDCA) released on April 14 show that the country has 731 new cases, of which 714 cases of infection in the community – the highest level in the country. Last 3 months. The current epidemic situation in Korea is considered to be at a level that should be considered by the government to upgrade the social gap, but considered it a “last resort” due to careful consideration of economic losses. practice.

In Europe, the epidemic is still complicated, with Turkey recording the highest number of new infections and deaths in a day ever. In the past 24 hours, the country recorded 59,187 new infections, and 273 deaths. To stop the spread of the epidemic, President Tayyip Erdogan announced a number of new restrictions and “partially closed” the country during the first two weeks of Ramadan.

After the state of emergency in the Czech Republic ended on April 12, the Czech Government was cautious in relaxing measures to prevent the COVID-19 epidemic. Accordingly, the Czech government still imposes a ban on gatherings on 2 people both indoors and outdoors, while emphasizing the concerns of epidemiologists about the rapid relaxation of measures that could be reversed. the positive trend of disease prevention.

Meanwhile, after seeing a significant improvement in the epidemic situation in the Czech Republic, Germany said it would end long-term border controls with the Czech Republic, which had been in place since February 14. Instead, Germany will continue to implement quarantine measures through intensive random inspections in the German-Czech border area.

The Norwegian government has also allowed restaurants and bars to return to serve alcohol until 10 p.m. daily. The Nordic country also allows people to receive up to 5 guests to play at home at the same time – an increase of 3 compared to the previous regulation, while the stadium will be able to host 600 people, but must divided into 3 areas. These rules and recommendations will apply throughout Norway, but high-risk areas such as the capital Oslo and surrounding areas can maintain stricter measures if needed. .

The Swiss government has announced it will significantly loosen the restrictions despite the fact that the country’s disease situation remains highly precarious and has even worsened in recent weeks. Accordingly, from the beginning of next week, restaurants and bars in Switzerland, which have been closed since December, 2020, will be reopened, applicable to the outdoor area. Movie theaters and other entertainment facilities will also be reopened with indoor and outdoor sports facilities.

Also on April 14, diplomatic sources said that EU member states had unanimously agreed to officially implement the vaccine passport initiative to reopen the tourism industry in the summer. 2021. This is part of an effort to restore to a new normal state while the COVID-19 epidemic is still spreading. Countries will discuss this initiative in detail with the European Parliament (EP) in May.

People wear masks to prevent the COVID-19 epidemic at El Alto-La Paz International Airport in Bolivia. Photo: AFP / VNA

In the Americas, the number of infections and deaths caused by the COVID-19 SARS-CoV-2 virus increased sharply in some South American countries such as Argentina, Uruguay, and Brazil. The Bolivian government announced the opening of a humanitarian corridor on the border with neighboring Brazil to facilitate the circulation of food and medicine. Bolivia closed its border with Brazil since April 2, to prevent the spread of a new variant of the SARS-CoV-2 virus that causes COVID-19 from neighboring countries.

Regarding the COVID-19 vaccine issue, US officials announced that the vaccination program is being accelerated with 3.3 million doses being injected per day. Meanwhile, the UK University of Oxford has decided to expand research in the combination use of COVID-19 vaccines to evaluate whether the combination of vaccines is safe and helps prolong immunity in humans. vaccinated or not.