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Can an Algorithm Predict the Pandemic’s Next Moves? – The New York Times

July 2nd, 2020

Judging when to tighten, or loosen, the local economy has become the world’s most consequential guessing game, and each policymaker has his or her own instincts and benchmarks. The point when hospitals reach 70 percent capacity is a red flag, for instance; so are upticks in coronavirus case counts and deaths.

But as the governors of states like Florida, California and Texas have learned in recent days, such benchmarks make for a poor alarm system. Once the coronavirus finds an opening in the population, it gains a two-week head start on health officials, circulating and multiplying swiftly before its re-emergence becomes apparent at hospitals, testing clinics and elsewhere.

Now, an international team of scientists has developed a model — or, at minimum, the template for a model — that could predict outbreaks about two weeks before they occur, in time to put effective containment measures in place.

In a paper posted on Thursday on arXiv.org, the team, led by Mauricio Santillana and Nicole Kogan of Harvard, presented an algorithm that registered danger 14 days or more before case counts begin to increase. The system uses real-time monitoring of Twitter, Google searches and mobility data from smartphones, among other data streams.

The algorithm, the researchers write, could function “as a thermostat, in a cooling or heating system, to guide intermittent activation or relaxation of public health interventions” — that is, a smoother, safer reopening.

“In most infectious-disease modeling, you project different scenarios based on assumptions made up front,” said Dr. Santillana, director of the Machine Intelligence Lab at Boston Children’s Hospital and an assistant professor of pediatrics and epidemiology at Harvard. “What we’re doing here is observing, without making assumptions. The difference is that our methods are responsive to immediate changes in behavior and we can incorporate those.”

Outside experts who were shown the new analysis, which has not yet been peer reviewed, said it demonstrated the increasing value of real-time data, like social media, in improving existing models.

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Updated 2020-07-03T05:57:13.472Z

The study shows “that alternative, next-gen data sources may provide early signals of rising Covid-19 prevalence,” said Lauren Ancel Meyers, a biologist and statistician at the University of Texas, Austin. “Particularly if confirmed case counts are lagged by delays in seeking treatment and obtaining test results.”

The use of real-time data analysis to gauge disease progression goes back at least to 2008, when engineers at Google began estimating doctor visits for the flu by tracking search trends for words like “feeling exhausted,” “joints aching,” “Tamiflu dosage” and many others.

The Google Flu Trends algorithm, as it is known, performed poorly. For instance, it continually overestimated doctor visits, later evaluations found, because of limitations of the data and the influence of outside factors such as media attention, which can drive up searches that are unrelated to actual illness.

Since then, researchers have made multiple adjustments to this approach, combining Google searches with other kinds of data. Teams at Carnegie-Mellon University, University College London and the University of Texas, among others, have models incorporating some real-time data analysis.

“We know that no single data stream is useful in isolation,” said Madhav Marathe, a computer scientist at the University of Virginia. “The contribution of this new paper is that they have a good, wide variety of streams.”

In the new paper, the team analyzed real-time data from four sources, in addition to Google: Covid-related Twitter posts, geotagged for location; doctors’ searches on a physician platform called UpToDate; anonymous mobility data from smartphones; and readings from the Kinsa Smart Thermometer, which uploads to an app. It integrated those data streams with a sophisticated prediction model developed at Northeastern University, based on how people move and interact in communities.

The team tested the predictive value of trends in the data stream by looking at how each correlated with case counts and deaths over March and April, in each state.

In New York, for instance, a sharp uptrend in Covid-related Twitter posts began more than a week before case counts exploded in mid-March; relevant Google searches and Kinsa measures spiked several days beforehand.

The team combined all its data sources, in effect weighting each according to how strongly it was correlated to a coming increase in cases. This “harmonized” algorithm anticipated outbreaks by 21 days, on average, the researchers found.

Looking ahead, it predicts that Nebraska and New Hampshire are likely to see cases increase in the coming weeks if no further measures are taken, despite case counts being currently flat.

“I think we can expect to see at least a week or more of advanced warning, conservatively, taking into account that the epidemic is continually changing,” Dr. Santillana said. His co-authors included scientists from the University of Maryland, Baltimore County; Stanford University; and the University of Salzburg, as well as Northeastern.

He added: “And we don’t see this data as replacing traditional surveillance but confirming it. It’s the kind of information that can enable decision makers to say, ‘Let’s not wait one more week, let’s act now.’”

For all its appeal, big-data analytics cannot anticipate sudden changes in mass behavior any better than other, traditional models can, experts said. There is no algorithm that might have predicted the nationwide protests in the wake of George Floyd’s killing, for instance — mass gatherings that may have seeded new outbreaks, despite precautions taken by protesters.

Social media and search engines also can become less sensitive with time; the more familiar with a pathogen people become, the less they will search with selected key words.

Public health agencies like the Centers for Disease Control and Prevention, which also consults real-time data from social media and other sources, have not made such algorithms central to their forecasts.

“This is extremely valuable data for us to have,” said Shweta Bansal, a biologist at Georgetown University. “But I wouldn’t want to go into the forecasting business on this; the harm that can be done is quite severe. We need to see such models verified and validated over time.”

Given the persistent and repeating challenges of the coronavirus and the inadequacy of the current public health infrastructure, that seems likely to happen, most experts said. There is an urgent need, and there is no lack of data.

“What we’ve looked at is what we think are the best available data streams,” Dr. Santillana said. “We’d be eager to see what Amazon could give us, or Netflix.”

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New strain of coronavirus spreads faster than original: study – DW (English)

July 2nd, 2020

The variation of COVID-19 currently dominating global cases is more infectious than the original strain that emerged in China, according to a new study published Thursday in thescientific journal Cell.

Results of lab-based research published in the journal suggested that the current mutation is more transmissible between people than the previous iteration of the virus, though the finding remains to be proven.

“I think the data is showing that there is a single mutation that actually makes the virus be able to replicate better, and maybe have high viral loads,” top US infectious disease specialist Anthony Fauci told the Journal of the American Medical Association about the study, which he was not involved in.

“We don’t have a connection to whether an individual does worse with this or not. It just seems that the virus replicates better and may be more transmissible, but this is still at the stage of trying to confirm that,” he said.

Read more: Chinese study warns new swine flu virus has ‘pandemic’ potential

Three to six times as infectious

Researchers from Los Alamos National Laboratory in New Mexico and Duke University in North Carolina partnered with the University of Sheffield’s COVID-19 Genomics UK research group. The scientists found the current variant of the virus — D614G — makes a small but significant change in the protein that protrudes from the surface of the virus that it uses to invade and infect human cells.

Initial results shared in April were criticized for not proving the mutation itself was responsible for its domination. Other factors or chance could have played a role, critics said

The research team carried out additional experiments, analyzing data of 999 British patients hospitalized with COVID-19. They observed that those with the variant had more viral particles in them, but it had no effect on the severity of their disease.

Laboratory experiments have, meanwhile, shown that the variant is three to six times more capable of infecting human cells.

Read more: Why do more men die from COVID-19?

Real-world implications remain unclear

At this stage, however, conclusions can only be considered “probable,” as such experiments often do not accurately replicate the dynamics of a pandemic. 

While the variant currently in circulation is considered more “infectious,” it is possible that it is less “transmissible” between people.

Virologist at the Yale School of Public Health Nathan Grubaugh, who was not involved in the study, said the results do not change much for the general public. 

“While there are still important studies needed to determine if this will influence drug or vaccine development in any meaningful way, we don’t expect that D614G will alter our control measures or make individual infections worse,” he wrote in a commentary piece.

“It’s more of a live look into science unfolding: an interesting discovery was made that potentially touches millions of people,” he added, “but we don’t yet know the full scope or impact.”

DW sends out a daily selection of the day’s news and features. Sign up here.

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Scientists say strain of coronavirus dominant around the world is different than what was seen in Wuhan | TheHill – The Hill

July 2nd, 2020

A strain of the coronavirus that was first seen in Italy is now the dominant strain of the virus, a group of scientists said Thursday.

In an article published by the peer-reviewed science journal Cell, researchers working with the Sheffield COVID-19 Genomics Group announced that the new strain “has become the most prevalent form in the global pandemic.”

The strain is different than what appeared in Wuhan, China, the city where the coronavirus is believed to have originated. 

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According to the science journal, tracking of the virus frequency revealed a prevalence of the dominant strain, labeled G614, that took over the prevalence of D614, the original strain.  

“Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to the introduction of the G614 variant,” the scientists wrote in their abstract, referring to the two strains.

“The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage,” they continued.

However, scientists cannot agree on the reasoning for the new strain’s dominance — researchers with the study suggested that the newer strain may be more virulent, while others contended in comments included with the study that the dominance could be due to its spread in the U.S.

The United States has largely failed to blunt its surge of new coronavirus infections recently, and now it has more confirmed cases than any other country.

Researchers of the study added that while their findings may indicate that the newer virus strain has a higher transmission rate, there was no evidence yet to suggest that it was a more severe strain than the one thought to have originated late last year in Wuhan. 

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“In infected individuals G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, although not with increased disease severity,” they wrote.

The U.S. now has more than 2.7 million confirmed cases of the virus, and on Thursday set another record for new coronavirus cases in a 24-hour period.

Italy, which was hit hard by the virus earlier this year, has largely seen its trend of new cases drop off and now reports under 200 per day across the country.

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Evo 2020 canceled after sexual misconduct allegations against co-founder – ESPN

July 2nd, 2020

Author Likens Meghan Markle, Prince Harry To Hitler In Unhinged Interview – HuffPost

July 2nd, 2020

Author and reality TV personality Lady Colin Campbell likened Meghan Markle and Prince Harry to Adolf Hitler in an unhinged interview Thursday. 

Campbell, who once claimed during a media appearance that convicted sex offender Jeffrey Epstein was not a pedophile, compared the royal couple to Hitler while speaking with “Access All Areas” hosts Joanna Chimonides and Stephen Leng on Fubar Radio. 

“I have no doubt that they tell themselves they’re doing the right thing, but we also need to remember that history is littered with people who thought they were doing good,” she said of the Sussexes. “I only have to mention Adolf Hitler, not that I’m putting them in the same camp as him.” 

“Adolf Hitler thought he was doing good for the world. Mao Zedong, who also killed hundreds of millions of his own people, he thought he was doing good,” she added. 

Campbell also surmised that the prince’s late mother, Princess Diana, would disapprove of the couple’s decisions. 

“Diana, for all her failings, was very royal,” the author said, adding that she would be “completely horrified” by the couple’s decision to step back as working members of the royal family and pursue financial independence. 

Lady Colin Campbell, here on a Fox special on Meghan Markle," says the couple just thinks they're doing the right thing.



Fox via Getty Images

Lady Colin Campbell, here on a Fox special on Meghan Markle,” says the couple just thinks they’re doing the right thing.

Campbell said that Meghan, whom she claimed was “overindulged” and “spoiled by her father,” set out making the plans for the couple to live in Los Angeles despite the prince’s public insistence that that was not the case.  

Campbell also speculated the couple was leaking their own press. 

“I mean, honestly. You know, I have never seen people rape their privacy to the extent that they have raped their own privacy on a daily basis,” she added. 

The 70-year-old, who once appeared on the reality show “I’m a Celebrity … Get Me Out of Here,” is one of the many who continue to attack the Duchess of Sussex, who has weathered misogynistic and racist attacks since she first began dating Prince Harry.

While Campbell, who also recently shamed a British news presenter for “living a lie” and coming out as gay later in life, has claimed that the duchess is a “fame addict” and that she has political aspirations to run for president one day. The Hitler comments, though, have escalated her baseless commentary to a new level of vile.

Meanwhile, the Sussexes have carried on with their charity efforts in Los Angeles and continue to speak up for racial justice amid the Black Lives Matter movement and ongoing protests and marches after the May 25 police killing of George Floyd in Minneapolis. 

Meghan recently spoke with Althea Bernstein, who is biracial and was the victim of an alleged hate crime by four white men in Wisconsin. The duchess talked to her about healing and staying off of social media during a 40-minute phone call, and she got the 18-year-old’s number to be able to check in with her again. 

The Duke and Duchess of Sussex meet children at the Commonwealth Day Service 2020 on March 9 in London.



Chris Jackson via Getty Images

The Duke and Duchess of Sussex meet children at the Commonwealth Day Service 2020 on March 9 in London.

The Duke of Sussex also gave an impassioned speech decrying institutional racism during a surprise appearance at the 2020 Diana Awards on Wednesday. 

“My wife said recently that our generation and the ones before us haven’t done enough to right the wrongs of the past. I too am sorry,” he said.

“Sorry that we haven’t got the world to the place that you deserve it to be. Institutional racism has no place in our societies. Yet it is still endemic. Unconscious bias must be acknowledged without blame to create a better world for all of you.” 

Together, the royal couple has also privately advocated for the Stop Hate for Profit campaign, according to Axios, which asks companies to pause spending advertising money on Facebook until the platform figures out a way to curb the spread of hate speech and disinformation. 

The NAACP praised the Sussexes for their solidarity with the campaign, as did Rashad Robinson, president of Color of Change, whose organization designs “campaigns powerful enough to end practices that unfairly hold Black people back, and champions solutions that move us all forward.” 

“I’ve appreciated the thoughtful conversations I’ve had with the Duke and Duchess,” Robinson said on Twitter. “Even more, I appreciate that they are using their platform to reach out to key corporations and share the goals of the #StopHateForProfit campaign.” 

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Scientists say strain of coronavirus dominant around the world is different than what originated in Wuhan | TheHill – The Hill

July 2nd, 2020

A strain of the coronavirus that was first seen in Italy is now the dominant strain of the virus, a group of scientists said Thursday.

In an article published by the peer-reviewed science journal Cell, researchers working with the Sheffield COVID-19 Genomics Group announced that the new strain “has become the most prevalent form in the global pandemic.” The strain is different than what appeared in Wuhan, China, the city where the coronavirus is believed to have originated. 

According to the science journal, tracking of the virus frequency revealed a prevalence of the dominant strain, labeled G614, that took over the prevalence of D614, the original strain.  

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“Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to the introduction of the G614 variant,” the scientists wrote in their abstract, referring to the two strains.

“The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage,” they continued.

However, scientists cannot agree on the reasoning for the new strain’s dominance — researchers with the study suggested that the newer strain may be more virulent, while others contended in comments included with the study that the dominance could be due to its spread in the U.S.

The United States has largely failed to blunt its surge of new coronavirus infections recently, and now it has more confirmed cases than any other country.

Researchers of the study added that while their findings may indicate that the newer virus strain has a higher transmission rate, there was no evidence yet to suggest that it was a more severe strain than the one thought to have originated late last year in Wuhan. 

“In infected individuals G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, although not with increased disease severity,” they wrote.

The U.S. now has more than 2.7 million confirmed cases of the virus, and on Thursday set another record for new coronavirus cases in a 24-hour period.

Italy, which was hit hard by the virus earlier this year, has largely seen its trend of new cases drop off and now reports under 200 per day across the country.

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Scientists say strain of coronavirus dominant around the world is different than what was seen in Wuhan – MSN Money

July 2nd, 2020


a person holding a baby in a blue room: Scientists say strain of coronavirus dominant around the world is different than what was seen in Wuhan
© getty: A medical worker takes a swab from a previously recovered COVID-19 coronavirus patient in Wuh… Scientists say strain of coronavirus dominant around the world is different than what was seen in Wuhan

A strain of the coronavirus that was first seen in Italy is now the dominant strain of the virus, a group of scientists said Thursday.

In an article published by the peer-reviewed science journal Cell, researchers working with the Sheffield COVID-19 Genomics Group announced that the new strain “has become the most prevalent form in the global pandemic.”

The strain is different than what appeared in Wuhan, China, the city where the coronavirus is believed to have originated.

According to the science journal, tracking of the virus frequency revealed a prevalence of the dominant strain, labeled G614, that took over the prevalence of D614, the original strain.

“Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to the introduction of the G614 variant,” the scientists wrote in their abstract, referring to the two strains.

“The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage,” they continued.

However, scientists cannot agree on the reasoning for the new strain’s dominance – researchers with the study suggested that the newer strain may be more virulent, while others contended in comments included with the study that the dominance could be due to its spread in the U.S.

The United States has largely failed to blunt its surge of new coronavirus infections recently, and now it has more confirmed cases than any other country.

Researchers of the study added that while their findings may indicate that the newer virus strain has a higher transmission rate, there was no evidence yet to suggest that it was a more severe strain than the one thought to have originated late last year in Wuhan.

“In infected individuals G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, although not with increased disease severity,” they wrote.

The U.S. now has more than 2.7 million confirmed cases of the virus, and on Thursday set another record for new coronavirus cases in a 24-hour period.

Italy, which was hit hard by the virus earlier this year, has largely seen its trend of new cases drop off and now reports under 200 per day across the country.

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Dominant Coronavirus Strain Appears to Be a Mutated, More Virulent Version, Study Finds – ScienceAlert

July 2nd, 2020

The genetic variation of the novel coronavirus that dominates the world today infects human cells more readily than the original that emerged in China, according to a new study published in the journal Cell on Thursday.

​The lab-based research suggests this current mutation is more transmissible between people in the real world compared to the previous iteration, but this hasn’t yet been proven.

​”I think the data is showing that there is a single mutation that actually makes the virus be able to replicate better, and maybe have high viral loads,” Anthony Fauci, the United States’s top infectious disease specialist, who wasn’t involved in the research, commented to Journal of the American Medical Association.

​”We don’t have a connection to whether an individual does worse with this or not. It just seems that the virus replicates better and may be more transmissible, but this is still at the stage of trying to confirm that,” he added.

​Researchers from the Los Alamos National Laboratory in New Mexico and Duke University in North Carolina partnered with the University of Sheffield’s COVID-19 Genomics UK research group to analyze genome samples published on GISAID, an international resource for sharing genome sequences.

​They found that the current variant, called “D614G”, makes a small but potent change in the “spike” protein that protrudes from the surface of the virus, which it uses to invade and infect human cells.

​The scientists first posted their paper to the medical preprint site bioRxiv in April, where it received 200,000 hits, a record.

​But it was initially criticized because the scientists had not proved that the mutation itself was responsible for its domination; it could have benefitted from other factors or from chance.

​The team therefore carried out additional experiments, many at the behest of the editors of Cell.

​They analyzed the data of 999 British patients hospitalized with COVID-19 and observed that those with the variant had more viral particles in them, but without this changing the severity of their disease.

​Laboratory experiments meanwhile showed that the variant is three to six times more capable of infecting human cells.

​”It seems likely that it’s a fitter virus,” said Erica Ollmann Saphire, who carried out one of the experiments at La Jolla Institute for Immunology.

​’This variant is the pandemic’

But everything at this stage can only be said to be “probable”: in vitro experiments often do not replicate the dynamics of a pandemic.

​As far as we know, although the variant circulating right now is more “infectious,” it may or may not be more “transmissible” between people.

​At any rate, said Nathan Grubaugh, a virologist at the Yale School of Public Health who was not part of the research: The expansion of the variant “whether through natural selection or chance, means that this variant now is the pandemic”.

​Writing in a commentary piece, Grubaugh added that, for the general public, these results don’t change much.

​”While there are still important studies needed to determine if this will influence drug or vaccine development in any meaningful way, we don’t expect that D614G will alter our control measures or make individual infections worse,” he said.

​”It’s more of a live look into science unfolding: an interesting discovery was made that potentially touches millions of people, but we don’t yet know the full scope or impact.”

© Agence France-Presse

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Captain America is now in Fortnite – The Verge

July 2nd, 2020

Rideau Hall: Canadian Armed Forces member arrested after breaching PM’s estate – BBC News

July 2nd, 2020
The main entrance to Rideau Hall in Ottawa, with a police car parked outsideImage copyright Getty Images
Image caption The main entrance to Rideau Hall in Ottawa appears to have been damaged

An armed member of Canada’s military has been arrested after driving a pick-up truck through the gates of an estate where Prime Minister Justin Trudeau lives, police say.

The suspect used his vehicle to breach the main entrance of Rideau Hall in Ottawa early on Thursday morning.

He then entered the grounds on foot before being confronted by police.

The man was arrested at 08:30 local time (12:30 GMT) without incident. He is in custody, with charges pending.

Mr Trudeau and his family, who are currently living at a cottage on the Rideau Hall estate while the prime minister’s official residence is being renovated, were not at home at the time of the incident.

Nor was Governor General Julie Payette, who resides at Rideau Hall as the official representative of Queen Elizabeth II, Canada’s head of state.

“We thank the RCMP and police for quickly resolving the situation this morning at Rideau Hall. All of our staff are safe,” Ms Payette tweeted on Thursday.

The Royal Canadian Mounted Police (RCMP) said the suspect was a member of the Canadian Armed Forces, whose identity “will be confirmed as soon as possible”.

Image copyright Getty Images
Image caption The suspect’s car was inspected by a bomb-disposal unit as a precaution

The RCMP said it is working closely with the Canadian Armed Forces to investigate the incident, which was resolved “quickly and safely”.

“Through our members’ vigilance, quick action and successful de-escalation techniques, this highly volatile incident was resolved swiftly and peacefully,” the RCMP’s deputy commissioner, Mike Duheme, said.

The grounds of Rideau Hall, which sits on an 88-acre (0.35 sq km) wooded estate, have been closed to the public during the coronavirus pandemic.

Pictures taken outside Rideau Hall appear to show damage to its main pedestrian gate, which the suspect rammed through in his vehicle. The vehicle was disabled on impact, the RCMP said.

Image copyright Getty Images
Image caption Mr Trudeau and his family live in a cottage on the grounds of the estate

Other pictures show an empty black pick-up truck inside the grounds of the estate. The RCMP said an army unit with a bomb-disposal robot searched the vehicle as a precaution.

Citing sources, Canadian media outlet Global News said the suspect had multiple firearms, including one rifle and two shotguns. The man indicated he wanted to speak to the prime minister but surrendered peacefully to police, a source told Global News.

CBC News cited a source as saying the suspect had driven his truck from the central province of Manitoba, about 1,900 km (1,180 miles) west of Ottawa.

Mr Trudeau has moved to limit the ownership of certain weapons in Canada, where gun ownership is popular, especially in rural parts of the country.

He introduced a long-promised ban on assault-style weapons in May this year, after a gun a rampage across the province of Nova Scotia that became the deadliest shooting in Canada’s history.

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Media captionTrudeau on weapons ban: “You don’t need an AR-15 to bring down a deer”

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