Tag Archives: Genomics

The study reveals how the SARS-CoV-2 B.1.1.7 variant entered the United States | Instant News


A team led by researchers from Yale School of Public Health has discovered how variant B.1.1.7 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first discovered in the UK, spread to several states in the United States. While the coronavirus pandemic has affected nearly every country around the world, the United States is currently in the lead with more than 27.8 million reported infections and the highest global death toll exceeding 2.4 million.

Kirsten St. George, Nathan D. Grubaugh and colleagues said that despite increased travel restrictions and increased testing for the coronavirus, the United States does not report the genome sequences of potential new variants of confirmed COVID-19 cases. Because the United States only accounts for 0.13% of COVID-19 cases, it was initially difficult to detect when variant B.1.1.7 first appeared in America.

“Sorting capacity varies widely across the country, and our travel data helps to disproportionately identify areas of B.1.1.7 cases that are underreported and where it would be prudent to immediately prioritize variant surveillance,” write the authors.

Study “Early recognition and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States” is available as preprint in medRxiv* server, when articles undergo peer review.

Track viruses

The researchers used a combination of October 2020 flight records from the UK to all United States airports and SARS-CoV-2 genomic sequencing to detect the origin of variant B.1.1.7 in the US. They argued that this time period was chosen because not only was it the most recent data available, but it also overlapped with the timing of variant B.1.1.7 originally thought to have spread throughout Great Britain.

According to the CDC’s February preliminary report, 33 states have confirmed 541 cases of B.1.1.7 in the United States. However, the authors argue that low genomic surveillance may not represent the true extent of variance. They instead analyzed the number of cases reported from December 2020 to January 2021 by the percentage of SARS-CoV-2 clinical samples taken.

Identification of areas at risk for imports B.1.1.7 and at risk of not being reported B.1.1.7.  A. Number of passengers arriving from Great Britain for the top 15 airports in October 2020 (labeled dots; size and color scale with population, see legend) shown on continental map of the United States (gray).  B. The bar plots represent the percentage of cases in each state during Dec 2020 and Jan 2021 (bottom x-axis; sourced from https://covidtracking.com/data) whose order was uploaded to GISAID.org (accessed February 4, 2021).  Bars are colored according to region (legend, top right).  The B.1.1.7 sequence sum for each state (upper x-axis; black dot) is determined by the pangolin lineage assignment in the GSIAID.org metadata.  CD.  The total number of passengers arriving from the UK in October 2020 to each state on the continental US was plotted against the SARS-CoV-2 (C) or B.1.1.7 SARS-CoV-2 (D) sequence numbers available on GISAID .org.  The dots are colored by region (legend from panel B).  The data used to create this image are listed in Data S1.

Identification of areas at risk for imports B.1.1.7 and at risk of not being reported B.1.1.7. A. Number of passengers arriving from Great Britain for the top 15 airports in October 2020 (labeled dots; size and color scale with population, see legend) shown on continental map of the United States (gray). B. Bar plots represent the percentage of cases in each state during Dec 2020 and Jan 2021 (bottom x-axis; sourced from https://covidtracking.com/data), the sequence uploaded to GISAID.org (accessed on 4 Feb 2021). Bars are colored according to region (legend, top right). The B.1.1.7 sequence sum for each state (upper x-axis; black dot) is determined by the pangolin lineage assignment in the GSIAID.org metadata. CD. The total number of passengers arriving from the UK in October 2020 to each state in the continental US was plotted against the sequence number SARS-CoV-2 (C) or B.1.1.7 SARS-CoV-2 (D) available on GISAID .org. The dots are colored according to the region (legend from panel B). The data used to create this image are listed in Data S1.

Strong evidence for the spread of the variant first came from New York

Low genomic surveillance was reported from December to January, with only 0.1% of COVID-19 cases sequenced and available to researchers. Twenty-six states had less than 0.1% of case sequences, and at the time of preprint publication, 14 states had yet to submit the genome sequences associated with B.1.1.7.

A large number of the B.1.1.7 strain was found in New York, California, and Florida. The ordering coincides with a large number of international flights coming from Great Britain to the state’s airports.

Multiple introductions, domestic spread, and community transmission B.1.1.7 SARS-CoV-2 in the United States.  A. Phylogeny maximum likelihood of B.1.1.7, including genome representatives from US, Europe, other global locations.  B. Highlights of the singletons and clades representing the direct introduction of B.1.1.7 from Europe, to different regions of the US, based on the same phylogenetic tree shown in (A).  A list of European to US transitions can be found in Data S1.  CE.  Time-based maximum likelihood phylogeny from different clades B.1.1.7 showing examples of domestic (C, E) and / or community transmission in New York (C), Connecticut (C), Michigan (C, D), and Illinois ( E).  A list of the SARS-CoV-2 sequences used in this study and author's thanks can be found in Data S2.

Multiple introductions, domestic spread, and community transmission B.1.1.7 SARS-CoV-2 in the United States. A. Phylogeny maximum likelihood of B.1.1.7, including genome representatives from US, Europe, other global locations. B. Highlights of the singletons and clades representing the direct introduction of B.1.1.7 from Europe, to different regions of the US, based on the same phylogenetic tree shown in (A). A list of European to US transitions can be found in Data S1. CE. Time-based maximum likelihood phylogeny from different clades B.1.1.7 showing examples of domestic (C, E) and / or community transmission in New York (C), Connecticut (C), Michigan (C, D), and Illinois ( E). A list of the SARS-CoV-2 sequences used in this study and the authors’ thanks can be found in Data S2.

From the three, the researchers concluded that New York was most likely the central hub for the incoming B.1.1.7 variant, which then spread to other states. The New York-New Jersey area has a record of 14,317 passengers to and from the UK. These results are consistent with the first case of COVID-19 with a new variant detected in Saratoga County, New York on December 24, 2020.

Since variant B.1.1.7 remains undetected, the researchers suggest continued community transmission is likely in New York, New Jersey, Connecticut, and Illinois from January 2021.

“So, increasing surveillance for B.1.1.7 and other variants through more conventional ordering and methods should be a high priority,” write the researchers.

Strong possibility of variant B.1.17 in other states

While the researchers sequenced most of the B.1.1.7 variant in New York, the investigators say that under-reporting may have contributed to undetected cases in other states. Their results showed Texas, Illinois and New Jersey had more than 2,500 people flying from England. However, all three states had 0.05% or less of cases sorted. The authors suggest a strong possibility that the spread of the new strain is increasing in other states.

“In places like New Jersey, Illinois, and Texas, however, if SARS-CoV-2 genomic surveillance could be improved, it might determine if B.1.1.7 cases were not reported disproportionately compared to New York and California,” wrote the researcher.

More genomic surveillance is needed for future research

Given limited travel data and low genomic surveillance, the researchers said the samples were too small to represent the full spread of this variant in the United States. In addition, they were unable to evaluate the level of transmission in the various areas and considered community distribution high. “In fact, local conditions and behavior played an important role in the formation of B.1.1.7, and may explain why cases are low in some states.”

As the spread of the new variant increases, the research team suggests increasing genome surveillance is a high priority task needed to reduce the spread of the virus.

* Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be construed as conclusions, guidelines for health-related clinical / behavioral practice, or are treated as defined information.

.



image source

The COVID-19 bill will improve the ability to recognize viral mutations | Instant News


WASHINGTON (AP) – TABLE ATTN: CAN BE ILLUSTRATED WITH JEFF ZIENTS ‘WHITE COORDINATOR ART FILE ART.

US scientists will gain a very broad range of capabilities to identify potentially lethal coronavirus mutations under the COVID-19 aid legislation that was advanced in Congress.

The US is now mapping the genetic makeup of only a fraction of positive virus samples, a situation some experts have likened to flying blind. This means the true domestic spread of the problematic mutation first identified in Britain and South Africa remains a suspect problem.

Such ignorance can be expensive. One concern is that a more contagious form like the British variant could move faster than the nation’s ability to get a vaccine into American hands.

“You have a small number of academic and public health laboratories that basically do genome surveillance,” said David O’Connor, AIDS researcher at the University of Wisconsin. “But there is no national coherence with the strategy.”

The Centers for Disease Control and Prevention is trying to herd those efforts in line with the government’s own continued detection work, but the COVID-19 law will take hunting to another level.

The bill approved for floor debate last week by the House Committee on Energy and Commerce will provide $ 1.75 billion for genome sequencing. It calls on the CDC to set up a national network to use technology to track the spread of mutations and guide public health precautions.

In the Senate, Wisconsin Democrat Tammy Baldwin has introduced legislation that will award $ 2 billion. Baldwin said the US should use gene mapping technology to analyze at least 15% of positive virus samples. It may not sound like much, but the current rate is believed to be 0.3% to 0.5%. Analyzing 15% of positive samples would expand surveillance by at least 30 times.

“Variants represent a growing threat,” said Baldwin. “At the start of the COVID-19 pandemic, increasing our testing capacity was critical to our ability to track and slow down the spread of the virus – the same is true for finding and tracing this variant.”

Genome sequencing basically involves mapping the DNA of an organism, key to its unique features. It’s done by high-tech machines that can cost from several hundred thousand dollars to $ 1 million or more. Trained technicians to run the machines and compute capacity to support the entire process add to costs.

In the case of the British variant which was first detected in the UK, changes to the virus have allowed it to spread more easily and are also believed to cause the more deadly disease COVID-19. The Institute for Health Metrics and Evaluation in Seattle reports that transmission of the British variant has been confirmed in at least 10 US states. CDC Director Dr. Rochelle Walensky told governors on Tuesday that it could become dominant by the end of March.

Sequencing 0.3% to 0.5% of virus samples, as the US is doing now, “doesn’t give us the ability to detect strains as they develop and become dominant,” said Dr. Phil Febbo, chief medical officer for Illumina, a San Diego-based company that develops genome sequencing technology.

The Biden administration must “set very clear goals,” he added. What hill are we going to ride?

“We need that data. Otherwise, in some ways, we are blind, ”said Esther Krofah, who directs the Milken Institute’s FasterCures initiative. “We don’t understand the prevalence of mutations which we should be worried about in the US”

Even more worrying than the British variant is the strain first detected in South Africa which scientists think may be at least partially resistant to some coronavirus vaccines. This variant has also been identified in the US in a limited number of cases.

White House coronavirus coordinator Jeff Zients called tracking virus mutations in the US “completely unacceptable,” saying the country was ranked 43rd in the world. But the Biden administration has not set a target for what level of viral gene mapping the country should strive for.

At the University of Wisconsin, AIDS scientist O’Connor said he and his colleagues began sequencing coronavirus samples from the Madison area “because that’s where we live”.

His colleague, virologist Thomas Friedrich, says the national effort will require more than money to buy a new genome sequencing machine. The CDC should set standards for state health officials and academic research institutions to fully share the information they get from analyzing virus samples. Currently, there are mixed state regulations and practices, and some of them restrict access to key details.

“We need to see this as the Manhattan Project or the Apollo program,” Friedrich said, referring to government-led scientific efforts that developed the atomic bomb and landed humans on the moon.

The UK was able to identify the variant because the national health system there has a coordinated gene mapping program that aims to sequence about 10% of the sample, he added. Since that happened, there has been greater urgency about genetic sequencing on this side of the Atlantic Ocean.

“The utility of doing this may not have been seen by many people until these variants started appearing,” says Friedrich.

.



image source

The E484K mutation is potentially linked to SARS-CoV-2 adaptive fitness | Instant News


A team of Brazilian scientists recently conducted a genomic and phylogenetic analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome to better understand the process of viral evolution. Their analysis revealed that the E484K mutation variant of SARS-CoV-2 was present in three different lineages in four regions of Brazil and that the mutation could serve as a general solution for viral evolution. Studies are currently available at bioRxiv* preprint server.

Background

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes Coronavirus disease 2019 (COVID-19), is a member of the Coronaviridae family, which is enveloped in positive sense single-strand RNA viruses with a larger genome size of about 30 kb. Since its appearance in December 2019 in China, researchers around the world have sequenced nearly 4.10,000 SARS-CoV-2 genomes and have shared information in the Global Initiative on Sharing All Influenza Data (GISAID) database.

Several epidemiological studies of the SARS-CoV-2 genomics have been conducted, with the majority focusing on viral mutations. spike protein, surface glycoproteins SARS-CoV-2 is responsible for binding to the host angiotensin-converting enzyme 2 (ACE2) and initiating viral entry. Current research mainly focuses on three viral lineages, B.1.1.7, B.1.351, and P.1. because of its significant impact on viral transmission and pathogenicity. From this lineage, the P.1 lineage is prevalent in Brazil with three mutations (K417T, E484K, and N501Y) in the spike receptor binding (RBD) domain. In Brazil, many viral genomes harbor the E484K mutation, which is associated with increased viral transmission and immune evasion.

In the current study, scientists evaluated mutation characteristics and phylogenetic relationships in currently known lineages in Brazil to understand the adaptive evolutionary process of SARS-CoV-2.

A mutation histogram frequently observed in the Brazilian SARS-CoV-2 genome which stores the E484K mutation.  The red label above the bar indicates the absolute nucleotide position and the blue label indicates the effect of this mutation on the corresponding protein.  Since P.1 has only 19 represented genomes and a handful of mutations, only the major mutations of concern were highlighted.  UTR: Areas that have not been translated;  Syn: Synonym substitution;  del: deletion;  ORF: Open Reading Frame;  Nsp: Non-structural protein;  S: Surge;  E: Envelope;  M: Membrane;  N: Nucleocapsid.

A mutation histogram frequently observed in the Brazilian SARS-CoV-2 genome that stores the E484K mutation. The red label above the bar indicates the absolute nucleotide position and the blue label indicates the effect of this mutation on the corresponding protein. Since P.1 has only 19 represented genomes and a handful of mutations, only the major mutations of concern were highlighted. UTR: Areas that haven’t been translated; Syn: Synonym substitution; del: deletion; ORF: Open Reading Frame; Nsp: Non-structural protein; S: Surge; E: Envelope; M: Membrane; N: Nucleocapsid.

An important observation

The results revealed that the SARS-CoV-2 variant with the E484K mutation was widespread in many regions in Brazil. This mutation was introduced in Brazil in October 2020. Because the E484K mutation was found in different viral lineages at the same time as other mutations, scientists suggest that this particular amino acid substitution could act as a general driver for viral evolution in different genetic variants of SARS. -CoV-2. In the E484K mutation, a negatively charged amino acid (glutamic acid) is replaced by a positively charged amino acid (lysine). Thus, it is hoped that mutations will have a significant impact on viral survival and adaptive evolution.

Structural analysis revealed that a new site for ACE2 (75 amino acid) binding was generated due to the E484K mutation. This appears to create a significantly stronger interaction between ACE2 and the native binding site located at the RBD and ACE2 interface (amino acid 501).

A very diverse range of genetic mutations was observed in all Brazilian lineages with the E484K mutation. On average, about 19 and 30 mutations were observed in lineages B.1.1.33 and P.1, respectively. Further genomic analysis of the most recently emerging P.2 lineage showed that the P.1 and P.2 lineages were rapidly developing and had been circulating in Brazil for a longer period.

A new specific single substitution analysis was also carried out in this study. One such mutation, A27V, is present in the N-terminal domain (NTD) of the spike protein. Research has suggested that mutations in the NTD spike can allosterically change the dynamics of the spike RBD-ACE2 interaction and facilitate immune evasion. In addition, evidence suggests that viral lineages carrying the E484K mutation are associated with increased escape from antibody-mediated neutralization. Although the true impact of E484K and other substitutes on immune avoidance remains unclear, scientists argue that the E484K mutation is associated with improved viral fitness under pressure of natural selection.

Learn significance

Overall, the study suggests that the E484K mutation acts as an important evolutionary event for different viral lineages in terms of increased viral fitness. The E484K mutation has the potential to increase the infectivity and immune-avoidance potential of SARS-CoV-2. According to scientists, further research investigating the effectiveness of human serum anti-SARS-CoV-2 against the E484K mutation variant of SARS-CoV-2 is urgently needed.

* Important Notice

bioRxiv publishes a preliminary scientific report that is not peer reviewed and, therefore, should not be construed as a conclusion, a guide to health-related clinical / behavioral practice, or be treated as prescribed information

.



image source

British Variant Spreads In US As Covid Mutations Increase | Instant News


Editor’s note: Find the latest COVID-19 news and guides on Medscape’s Coronavirus Resource Center.

The British B117 variant is circulating in at least 24 states, according to new data from the surveillance of the COVID-19 Centers for Control and Prevention (CDC) variant. The CDC projects that the British variant will become the dominant strain in the United States by March.

From any point of view, the UK appears to be on the crosshairs of COVID-19: Weeks after a new, highly contagious variant emerged that sparked a spike in cases and a new lockdown, Britain is declared to have the world’s highest death rate from coronavirus.

But Britain also has a less secretive weapon: the genome sequencing program that is widely believed to be the most coordinated and advanced any country has ever created. In the grip of the virus, the British have gathered important insights into the behavior and consequences of SARS-CoV-2.

But B117 is also important for what’s missing: In this case, it results in a negative result on certain PCR tests on the spike protein, or S gene.

One of the S gene mutations specific to the variant deletes two amino acids, causing that portion of the PCR test to be negative. The coincidental finding known as target failure of the S gene has become an integral proxy to help track where and when the variant spread in the UK, where about 5% of samples from COVID-19 infected patients are sequenced, said Sharon Peacock. , PhD, executive director and chair of the COVID-19 Genomics UK Consortium.

The same tactic could prove valuable for doctors overwhelmed by cases and deaths, but lacking high-level sequence information about the virus, Peacock said. Medscape Medical News. A British report released on Friday stated that there was a “realistic possibility” that the variant had a higher death rate than other SARS-CoV-2 cases.

“In this particular variant, the deletion of the genome causes one part of the diagnostic test to fail,” explains Peacock. “Some targets are positive, but these are negative. In the UK, this has been used as a substitute marker.”

Targeting Unseen Enemies

B117 isn’t the only variant producing these results, Peacock warns, “but in screening for it, you can think about it.”

“Because the UK ranks about 5% of the cases they detect, this gives them very important clues about what’s going on there,” says Anderson Brito, PhD, a virologist and postdoctoral researcher at Yale University School of Public Health in New Haven. , Connecticut, where investigators created a special PCR test to detect the B117 variant.

Brito, who lived in the UK for 4 years while studying for a doctorate at Imperial College London, said a “major advantage” was a more integrated process for collecting and sequencing samples. Important information – including date and place of collection – is included with each sample, which encourages not only sorting, but also an epidemiological perspective.

“They weren’t in the dark at all,” said Brito Medscape Medical News. “I don’t think any other country in the world knows better which lineage of the virus is circulating.”

CDC launches the file SPHERES a consortium in May 2020 to coordinate the sequencing of the SARS-CoV-2 genome across the United States.

But the American genome effort was “not concentrated,” said Brito, whose lab detected the first two cases of the British variant in Connecticut on January 6. “We had difficulty getting samples, because they were decentralized to a level where there was little coordination between hospitals and research centers. They were not as connected as in the UK. If we only get samples and have no collection date and no origin information, for example, it is at basically useless. “

Global genome collaboration incl GISAID, an international database where researchers share new genomes of various coronaviruses. By mid-January, the United States had shipped about 68,000 sequences to GISAID, added about 3,000 new samples each week and expects more from commercial laboratories in the coming days, according to the CDC.

“The UK must have been much more looking for variants when they emerged,” says Gigi Gronvall, PhD, immunologist and senior scholar at the Johns Hopkins Center for Health Security in Baltimore. “The US has now changed it.”

Warning From British Scientists to the World

Despite these genomic achievements, some British scientists say they are sorry too, hoping they would know how fast SARS-CoV-2 actually spread a year ago, when it hit western Europe.

That information is critical not only for prevention efforts, but because the virus is sure to mutate more quickly the more people become infected, says Igor Rudan, MD, PhD, director of the Center for Global Health Research at the University of Edinburgh in the UK.

“Italy showed us how fast it is spreading and how deadly it is for the very old and people with many comorbidities,” said Rudan, who is also the editor in chief of Journal of Global Health. “We hope we know it is spreading so fast, and we hope we know the threshold of cases we can allow to be infected before the virus mutates.”

More mutations meant more new strains of SARS-CoV-2, Rudan said Medscape Medical News. “We have reached that threshold now and will see more of these mutations,” he said.

Despite its current struggles, Britain is trying to go beyond tracking the spread of its new variant and trying to identify new mutations that might change the way the virus behaves.

Three features of each of the variants that emerged were very important, explains Peacock: Is it more contagious? Is it more deadly? And does that bypass the natural or vaccine-induced ability of immunity to protect people from infection?

“We need to sort the people who come to the hospital who are sick,” said Peacock, also a professor of public health and microbiology at the University of Cambridge, UK. “Also, if anyone gets infected after they’ve gotten sick or got vaccinated, we really want to know what it looks like” genomically.

SARS-CoV-2 has recorded more than 4000 mutations, Peacock said. But “knowing that viruses mutate all the time is not reason enough not to look. We really wanted to know whether mutations cause changes in amino acids, and whether they can cause functional changes,” he said.

However, for now, experts say they are relieved that the British strain does not appear to be able to avoid the COVID-19 vaccine or make it less effective.

“Although mutations are common, those that can change the virus code are rare,” explains Brito. If necessary, the vaccine can be changed to replace the spike gene sequence “in a matter of weeks,” he said. “We’ve done this for flu vaccine. Every year, we have to monitor the variants of the virus in circulation to develop a vaccine that covers most of these viruses. If we end up doing it for SARS-CoV-2, I won’t be surprised. “

But the increase in variant-triggered infections will require more people to be vaccinated before herd immunity can be achieved, Rudan warned. “If it spreads faster, we need to vaccinate maybe 85% of people vs 70% to achieve herd immunity,” he said.

One lesson the COVID-19 pandemic brings with it “is to always be vigilant about what happens next,” said Peacock. Although confident about the genome effort in Britain to date, he and his colleagues feel they are still trying to fully understand the evolutionary changes of the virus.

“We’re ahead of the curve right now, but we want to be ahead of the curve,” said Peacock. “It is very important to be ahead of what might happen because we don’t know how the virus will develop.”

Follow Medscape on Facebook, Indonesia, Instagram, and Youtube

.



image source

The new N501 SARS-CoV-2 mutation may have been circulating in Italy since August 2020 | Instant News


A recent study published in Lancet Infectious Disease The journal suggests that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain mutated by substitution at position 501 may have been circulating unnoticed even before the end of September 2020, when the rapid emergence of the B.1.1.7 lineage (carrying the N501Y mutation) was initially reported.

On 14 December 2020, British authorities reported to the World Health Organization (WHO) that a new variant of SARS-CoV-2, the causative agent for the ongoing coronavirus disease 2019 (COVID-19) pandemic, was identified through the viral genome sequence.

This variant is often referred to as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, 2020, month 12, variant 01), was shown to spread more easily among people, although there was no significant association with symptom severity or vaccines efficacy.

However, the mutation is a viral spike type glycoproteins characteristics for this variant, with N501Y a major concern as it involves one of the six major amino acid residues which is responsible for the close contact between the SARS-CoV-2 receptor-binding domain (RBD) and cellular angiotensin-converting enzyme 2 (ACE2). receptors.

As a result, a group of researchers, led by Dr. Simona Fiorentini of the Department of Molecular and Translational Medicine at the University of Brescia in Italy, performed a detailed metagenomic sequencing and bioinformatic analysis to take an in-depth look at Italian isolates.

Detailed genetic characterization

In November 2020, a 59-year-old man with a history of SARS-CoV-2 infection continued to undergo molecular testing. After laboratory confirmation of the infection, genetic characterization of the virus in the November or MB61-Nov samples (but also the previous sample from August 2020, known as MB61-August) was carried out by metagenomic sequencing.

The two complete genomes obtained were then compared with the complete viral genomes freely available at GISAID platform, which is an open source of access to genome data for the influenza virus and SARS-CoV-2.

Strains with the N501Y mutation in spike RBD, recently characterized in Italy and Great Britain as belonging to the rapidly emerging B.1.1.7 lineage, were included in the analysis. Finally, sequence alignment and detailed editing are also carried out to get a complete picture.

The N501T variant arrived in early August

In summary, the bioinformatic analysis in this study revealed that the MB61-Aug SARS-CoV-2 isolate had accumulated ten amino acid changes compared to the initial Italian isolate; In addition, three more have appeared as it evolves until the end of November 2020.

It should be noted that the substitution of N501T was found in the MB61-Aug and MB61-Nov SARS-CoV-2 isolates, which leads to the conclusion that mutations in the key amino acid 501 residue have been spreading in Italy since August 2020..

Our maximum possible time scale tree shows that the N501T variant of this spike appeared in early August in northern Italy, and therefore the SARS-CoV-2 strain having a substitution at position 501 may have been circulating unnoticed even before the end of September 2020, when the Lineage A rapidly emerging B.1.1.7 (carrying the N501Y mutation) was first reported, “the study authors said.

The need for massive research efforts

Recent discoveries regarding the evolution of SARS-CoV-2, particularly in RBD, require massive scientific efforts to pinpoint new variants with the potential for increased spread of the virus, but also with a tendency to exhibit evasive behavior towards strains of infection or vaccines. induced neutralizing immunity.

This study is one step in that direction, and also compares the Wuhan reference strain with the two MB61 variants. The variant actually carries four mutations and one deletion to the glycoprotein spike – two of which are located within the RBD.

Nonetheless, more complex and lengthy studies requiring collaboration between different research groups will be needed in the future. In this regard, the recently established WHO SARS-CoV-2 Virus Evolution Working Group is a way to increase understanding of this timely problem.

Source:

Journal reference:

.



image source