How biological detective work can reveal who engineered a virus

Asia's Tech News Daily

SARS-CoV-2, the virus that causes Covid-19, wasn’t intentionally created in a lab. We don’t have much evidence one way or the other whether its emergence into the world was the result of a lab accident or a natural jump from animal to human, but we know for sure that the virus is not the product of deliberate gene editing in a lab.

How biological detective work can reveal who engineered a virus
© Frederick Florin/AFP via Getty Images Bio labs leave their distinctive traces on DNA and RNA they engineer.

How do we know that? Bioengineering leaves traces — characteristic patterns in the RNA, the genetic code of a virus, that come from splicing in genes from elsewhere. And investigations by researchers have definitively shown that the novel coronavirus behind Covid-19 doesn’t bear the hallmarks of such manipulation.

That fact about bioengineered viruses raises an interesting question: What if those traces that gene editing leave behind were more like fingerprints? That is, what if it’s possible not just to tell if a virus was engineered but precisely where it was engineered?

That’s the idea behind genetic engineering attribution: the effort to develop tools that let us look at a genetically engineered sequence and determine which lab developed it. A big international contest among researchers earlier this year demonstrates that the technology is within our reach — though it’ll take lots of refining to move from impressive contest results to tools we can reliably use for bio detective work.

The contest, the Genetic Engineering Attribution Challenge, was sponsored by some of the leading bioresearch labs in the world. The idea was to challenge teams to develop techniques in genetic engineering attribution. The most successful entrants in the competition could predict, using machine-learning algorithms, which lab produced a certain genetic sequence with more than 80 percent accuracy, according to a new preprint summing up the results of the contest.

This may seem technical, but it could actually be fairly consequential in the effort to make the world safe from a type of threat we should all be more attuned to post-pandemic: bioengineered weapons and leaks of bioengineered viruses.

One of the challenges of preventing bioweapon research and deployment is that perpetrators can remain hidden — it’s difficult to find the source of a killer virus and hold them accountable.

But if it’s widely known that bioweapons can immediately and verifiably be traced right back to a bad actor, that could be a valuable deterrent.

It’s also extremely important for biosafety more broadly. If an engineered virus is accidentally leaked, tools like these would allow us to identify where they leaked from and know what labs are doing genetic engineering work with inadequate safety procedures.

The fingerprint of a virus

Hundreds of design choices go into genetic engineering: “what genes you use, what enzymes you use to connect them together, what software you use to make those decisions for you,” computational immunologist Will Bradshaw, a co-author on the paper, told me.

“The enzymes that people use to cut up the DNA cut in different patterns and have different error profiles,” Bradshaw says. “You can do that in the same way that you can recognize handwriting.”

Because different researchers with different training and different equipment have their own distinctive “tells,” it’s possible to look at a genetically engineered organism and guess who made it — at least if you’re using machine-learning algorithms.

The algorithms that are trained to do this work are fed data on more than 60,000 genetic sequences different labs produced. The idea is that, when fed an unfamiliar sequence, the algorithms are able to predict which of the labs they’ve encountered (if any) likely produced it.

A year ago, researchers at altLabs, the Johns Hopkins Center for Health Security, and other top bioresearch programs collaborated on the challenge, organizing a competition to find the best approaches to this biological forensics problem. The contest attracted intense interest from academics, industry professionals, and citizen scientists — one member of a winning team was a kindergarten teacher. Nearly 300 teams from all over the world submitted at least one machine-learning system for identifying the lab of origin of different sequences.

In that preprint paper (which is still undergoing peer review), the challenge’s organizers summarize the results: The competitors collectively took a big step forward on this problem. “Winning teams achieved dramatically better results than any previous attempt at genetic engineering attribution, with the top-scoring team and all-winners ensemble both beating the previous state-of-the-art by over 10 percentage points,” the paper notes.

The big picture is that researchers, aided by machine-learning systems, are getting really good at finding the lab that built a given plasmid, or a specific DNA strand used in gene manipulation.

The top-performing teams had 95 percent accuracy at naming a plasmid’s creator by one metric called “top 10 accuracy” — meaning if the algorithm identifies 10 candidate labs, the true lab is one of them. They had 82 percent top 1 accuracy — that is, 82 percent of the time, the lab they identified as the likely designer of that bioengineered plasmid was, in fact, the lab that designed it.

Top 1 accuracy is showy, but for biological detective work, top 10 accuracy is nearly as good: If you can narrow down the search for culprits to a small number of labs, you can then use other approaches to identify the exact lab.

There’s still a lot of work to do. The competition looked at only simple engineered plasmids; ideally, we’d have approaches that work for fully engineered viruses and bacteria. And the competition didn’t look at adversarial examples, where researchers deliberately try to conceal the fingerprints of their lab on their work.

How genetic fingerprinting can keep the world safer

Knowing which lab produced a bioweapon can protect us in three ways, biosecurity researchers argued in Nature Communications last year.

First, “knowledge of who was responsible can inform response efforts by shedding light on motives and capabilities, and so mitigate the event’s consequences.” That is, figuring out who built something will also give us clues about the goals they might have had and the risk we might be facing.

Second, obviously, it allows the world to sanction and stop any lab or government that is producing bioweapons in violation of international law.

And third, the article argues, hopefully, if these capabilities are widely known, they make the use of bioweapons much less appealing in the first place.

But the techniques have more mundane uses as well.

Bradshaw told me he envisions applications of the technology could be used to find accidental lab leaks, identify plagiarism in academic papers, and protect biological intellectual property — and those applications will validate and extend the tools for the really critical uses.

It’s worth repeating that SARS-CoV-2 was not an engineered virus. But the past year and a half should have us all thinking about how devastating pandemic disease can be — and about whether the precautions being taken by research labs and governments are really adequate to prevent the next pandemic.

The answer, to my mind, is that we’re not doing enough, but more sophisticated biological forensics could certainly help. Genetic engineering attribution is still a new field. With more effort, it’ll likely be possible to one day make attribution possible on a much larger scale and to do it for viruses and bacteria. That could make for a much safer future.

A version of this story was initially published in the Future Perfect newsletter. Sign up here to subscribe!

Internet Explorer Channel Network
Asia's Tech News Daily
News Related

OTHER NEWS

Strictly's Craig Revel Horwood ‘in row with BBC as he uses show catchphrase in bed advert'

STRICTLY judge Craig Revel Horwood has come under fire for using his famous Strictly catchphrase in an advert for bed company Dreams. The BBC has strict rules against its stars ... Read more »

5 Ways To Cook With Parchment Paper

Fish with salad Photo: 123RF Parchment paper is used to line baking pans as it is coated with silicon, which makes it non-stick – ideal for baking cookies and brownies. ... Read more »

Valneva Comments on COV-Boost Clinical Trial Data

Saint Herblain (France), December 3, 2021 – Valneva SE (Nasdaq: VALN; Euronext Paris: VLA), a specialty vaccine company, today responded to data published from the COV-Boost COVID-19 vaccine trial, which ... Read more »

The Masked Singer 2022 characters announced including Bagpipes and Robobunny

The Masked Singer has revealed the 12 new characters that will make up the performers for the new series of the ITV show. There will be a new winner crowned ... Read more »

Parts of King County seeing higher demand for vaccines

Those looking to get a COVID booster have been struggling to find a timely appointment. Read more »

Salem police charge man after dead body discovered in trunk

One person was arrested after Salem Police found a suitcase in a car contained a deceased person. According to Salem Police, officers responded Thursday morning to the Claxter Court Apartments ... Read more »

SFPD search for shooter

Dec. 3—Santa Fe police are searching for a shooter who wounded a man Wednesday evening near the 1200 block of Senda del Valle. Officers were dispatched to the area around ... Read more »

Omicron coronavirus variant could slow economic growth, warns IMF chief

© Provided by dw.com Georgieva called for debt restructuring and a reduction in tariffs The new omicron variant of COVID-19 could slow the global economic recovery, International Monetary Fund (IMF) ... Read more »

More than 40,000 kids 5-11 have gotten COVID vaccine at NYC schools

The city started offering vaccines to kids at school in November. Brigitte Stelzer More than 40,000 kids ages 5 to 11 have received coronavirus vaccines at city schools, the Department ... Read more »

The Devastating Death Of West Side Story's Yvonne Wilder

United Artists Yvonne Wilder, the actress known for role as Consuelo in 1961’s “West Side Story,” has died at the age of 84, according to Variety. The publication further reports ... Read more »

Europe hits 75 million COVID cases as it braces for Omicron: Live

© Provided by Al Jazeera A rise in the prevalence of COVID-19 infections in England in the latest week was driven by the dominant Delta variant rather than Omicron, Britain’s ... Read more »

Money, money, money: ABBA sues over Abba Mania cover band

© Reuters/LISI NIESNER FILE PHOTO: ABBA: Super Troupers The Exhibition By Jonathan Stempel NEW YORK (Reuters) – The Swedish pop supergroup ABBA on Friday filed a lawsuit to stop a ... Read more »

Car review: Genesis GV80 – the budget Bentley lookalike

So there I was making my way back to the car park near the shops in Oadby to enjoy another drive in the lovely Genesis GV80 and what should I ... Read more »

Oxford High School student escaped likely death by running from bathroom, source says

An Oxford High School student narrowly escaped potential death in Tuesday's tragedy by running from a boy's bathroom where a classmate was fatally shot, the Free Press has learned. A ... Read more »

Involuntary manslaughter: What charges mean against Oxford shooting suspect's parents

Prosecutors have charged the parents of a teen accused of gunning down his classmates at Oxford High School earlier this week, according to court records filed Friday. Online records for ... Read more »

Des Moines police investigating rumored threat of weapon at Roosevelt High School

Des Moines police are investigating the source of a rumored threat of a weapon being brought to school at Roosevelt High School and have provided additional security at the school ... Read more »

Jack Fincham sparks rumours he's secretly reunited with ex Chloe Brockett as he shares bed selfie to say happy birthday

JACK Fincham has sent the rumour mill into overdrive after posting a picture of himself and Chloe Brockett in bed together. The former Love Island star, 30, posted the snap ... Read more »

Xian Gaza dares Diego Loyzaga to admit courting Barbie Imperial, AJ Raval simultaneously

Via a facebook post on Tuesday, November 30, social media personality Xian Gaza urged Diego Loyzaga to admit that he courted Barbie Imperial and AJ Raval simultaneously. © Provided by ... Read more »

61-year-old govt employee gets permanent post after 23 years

SIXTY-one-year-old Joseph Lappay finally gets a permanent appointment after more than 23 years working in government service in the province of Abra. This was posted in the Facebook page named ... Read more »

Parents of Oxford school shooting suspect charged with involuntary manslaughter

As news broke Tuesday of a mass shooting at Oxford High School, the mother of the teen suspect sent her son a text message. “Ethan, don't do it,” Jennifer Crumbley ... Read more »

Karina Bautista reaps good feedback on her acting despite being a newbie in showbiz

Kapamilya star Karina Bautista couldn’t help, but express her gratitude for the compliments she got from netizens for her breakthrough performance as Bea in ABS-CBN’s trending series Viral Scandal. © ... Read more »

Cyclone Jawad set to impact Andhra Pradesh, Odisha from today

© Provided by The Times of India NEW DELHI: National Disaster Response Force (NDRF) and other central/state agencies were deployed in strength on Friday for relief and rescue operations in ... Read more »

Elderly Asian man who was kicked while in his walker at the beginning of COVID faces attacker in court

Nearly two years after an attack that required multiple stitches to his head, an 84-year-old Asian man reportedly met his alleged attacker for the first time in court on Thursday. ... Read more »

Wichita Falls man convicted of two counts of child rape

A jury took less than 15 minutes Friday to find a Wichita Falls man guilty of raping a 10-year-old boy in 2016 at his home. Nelson Head Nelson Christopher Head, ... Read more »

Police arrest burglary suspect

Dec. 3—VALDOSTA — Police arrested a burglary suspect Wednesday. At about 11 a.m., officers responded to Loganberry Circle after a woman called 911 to report a break-in, the Valdosta Police ... Read more »

COVID-19: Pfizer and Moderna jabs give best overall boost, UK study finds

The Pfizer and Moderna vaccines being used in the UK as boosters prompt the best overall response, according to a UK trial. The study, published in the Lancet, involved almost ... Read more »

Thousands of homes face second weekend without power

Thousands of people are facing a second weekend without power as further cold weather is predicted to hit the UK. Homes across parts of Scotland and the North East and ... Read more »

Chhattisgarh FIR against Covid positive man who broke isolation and went to Mumbai

© Provided by The Times of India The Bilaspur administration has registered an FIR against a 31-year-old man who tested positive for Covid after returning from the Maldives, but broke ... Read more »

Goldman CEO defends DJ'ing habit, admits Barry Manilow a ‘guilty pleasure'

David Solomon said the first record he bought was a sountrack of American Graffiti. FilmMagic for Sports Illustrated Goldman Sachs CEO David Solomon defended his side gigs as a dance-club ... Read more »

The Supreme Court isn't a medical board or legislature — it shouldn't make abortion law

People demonstrate in front of the Supreme Court this week as the court hears arguments in a Mississippi case where a 2018 law would ban abortions after 15 weeks of ... Read more »

Ad revenue: Facebook and Google make more than top 10 media firms put together

© Provided by The Indian Express That online advertising was gradually chipping away from other media was known, but the latest advertisement revenues from the India operations of BigTech companies ... Read more »

Godrej Properties Rating: Buy- Leadership position is well deserved

© Provided by The Financial Express In fact, considering that GPL ranks the highest in Pune and the NCR by share of launches since FY20, it would gain additional market ... Read more »

Delhi's air marginally cleaner day after drizzle, strong winds

© Provided by Hindustan Times Since November this year, Delhi has been reeling under some of the worst pollution spells it has experienced since air quality monitoring began. (ANI file ... Read more »

Jawad to be first cyclone to hit Odisha in December in 130 years

© Provided by The Times of India BHUBANESHWAR: If Cyclone Jawad hits Odisha coast on Sunday as predicted, it will be the first one to do so to the state ... Read more »

Dickert introduced as Wash St football coach; 3-2 as interim

Washington St Dickert Football (©Lewiston Tribune) Jake Dickert was introduced Thursday as the new head football coach at Washington State and vowed to “bring the Pac-12 championship back here to ... Read more »

Shooter in Colorado rampage that killed 10 deemed unfit to stand trial

FILE PHOTO: Ahmad Al Aliwi Alissa, suspect in King Soopers shooting, appears in a Boulder County District Court By Keith Coffman DENVER (Reuters) – A Colorado judge on Friday ruled ... Read more »

Mum with terminal cancer 'desperate' to make it to Christmas and son's 18th birthday

Hayley Adams says she’s ‘Christmas mad’ – she’s even known as ‘Miss Christmas’ to her friends and family. But this year there’s only one present she really wants. The terminally ... Read more »

Jan. 6 panel postpones deposition with former DOJ official

© Provided by Associated Press House Jan. 6 Select Committee Chairman Bennie Thompson, D-Miss., center, flanked by Rep. Zoe Lofgren, D-Calif., left, and Vice Chair Liz Cheney, R-Wyo., meet to ... Read more »

Glentoran boss Mick McDermott: Jay Donnelly on top of his game is best striker in Irish League

Glentoran manager Mick McDermott believes penalty box poacher Jay Donnelly in top form is the Irish League’s deadliest striker. Donnelly has scored a prolific 31 goals in 57 games for ... Read more »

Brazil's Bolsonaro investigated for linking vaccine and AIDS

BRASILIA, Brazil — BRASILIA, Brazil — A justice of Brazil’s top court ordered on Friday that President Jair Bolsonaro be investigated for comments linking COVID-19 vaccines to AIDS — an ... Read more »
On free-english-test.com you will find lots of free English exam practice materials to help you improve your English skills: grammar, listening, reading, writing, ielts, toeic