Analysis-In mutant variants, has the coronavirus shown its best tricks?

By Kate Kelland and Julie Steenhuysen

LONDON/CHICAGO (Reuters) – The rapid rise in different parts of the world of deadly, more infectious coronavirus variants that share new mutations is leading scientists to ask a critical question – has the SARS-CoV-2 virus shown its best cards?

New variants first detected in such far-flung countries as Brazil, South Africa and Britain cropped up spontaneously within a few months late last year. All three share some of the same mutations in the important spike region of the virus used to enter and infect cells.

These include the E484k mutation, nicknamed “Eek” by some scientists for its apparent ability to evade natural immunity from previous COVID-19 infection and to reduce protection offered by current vaccines – all of which target the spike protein.

The appearance of similar mutations, independent of one another, springing up in different parts of the globe shows the coronavirus is undergoing “convergent evolution,” according to a dozen scientists interviewed by Reuters.

Although it will continue to mutate, immunologists and virologists said they suspect this coronavirus has a fixed number of moves in its arsenal.

The long-term impact for the virus’ survival, and whether a limit on the number of mutations makes it less dangerous, remains to be seen.

“It is plausible that this virus has a relatively limited number of antibody escape mutations it can make before it has played all of its cards, so to speak,” said Shane Crotty, a virologist at the La Jolla Institute for Immunology in San Diego.

That could enable drugmakers to stay on top of the virus as they develop booster vaccines directly targeting current variants, while governments struggle to tame a pandemic that has killed nearly 3 million people.

The idea that the virus could have a limited number of mutations has been circulating among experts since early February, and gathered momentum with the posting of a paper showing the spontaneous appearance of seven variants in the United States, all in the same region of the spike protein.

EVOLUTION, IN REAL TIME

The process of different species independently evolving the same traits that improve survival odds is central to evolutionary biology. The vast scope of the coronavirus pandemic – with 127.3 million infections globally – allows scientists to observe it in real time.

“If you wanted to sort of write a little textbook about viral evolution, it’s happening right now,” Dr. Francis Collins, a geneticist and director of the U.S. National Institutes of Health, said in an interview.

Scientists saw the process on a smaller scale in 2018 as a dangerous H7N9 bird flu virus in China appeared to begin adapting to human hosts. But no pathogen has evolved under such global scrutiny as SARS-CoV-2.

Wendy Barclay, a virologist and professor at Imperial College London and a member of a scientific advisory panel to the UK government, said she is struck by the “amazing amount of convergent evolution we’re seeing” with SARS-CoV-2.

“There are these infamous mutations – E484K, N501Y and K417N – which all three variants of concern are accumulating. That, added together, is very strong biology that this is the best version of this virus in the given moment,” Barclay said.

It’s not that this coronavirus is especially clever, scientists said. Each time it infects people it makes copies of itself, and with each copy it can make mistakes. While some mistakes are insignificant one-offs, the ones that give the coronavirus a survival advantage tend to persist.

“If it keeps happening over and over again, it must be providing some real growth advantage to this virus,” Collins said.

Some specialists believe the virus may have a limited number of mutations it can sustain before compromising its fitness – or changing so much it is no longer the same virus.

“I don’t think it’s going to reinvent itself with extra teeth,” said Ian Jones, a professor of virology at Britain’s University of Reading.

“If it had an unlimited number of tricks…we would see an unlimited number of mutants, but we don’t,” said Michel Nussenzweig, an immunologist at Rockefeller University in New York.

CAUTIOUS OPTIMISM

Scientists remain cautious, however, and say predicting how a virus will mutate is challenging. If there are limits on how the coronavirus can evolve, that would simplify things for vaccine developers.

Novavax Inc is adapting its vaccine to target the South African variant that in lab tests appeared to render current vaccines less effective. Chief Executive Stan Erck said the virus can only change so much and still bind to human hosts, and hopes the vaccine will “cover the vast majority of strains that are circulating.”

If not, Novavax can continue matching its vaccine to new variants, he said.

Researchers are tracking the variants through data-sharing platforms such as the Global Initiative on Sharing Avian Flu Data, which houses a huge trove of coronavirus genomes.

Scientists recently identified seven U.S. coronavirus variants with mutations all occurring in the same location in a key portion of the virus, offering more evidence of convergent evolution.

Other teams are conducting experiments that expose the virus to antibodies to force it to mutate. In many cases, the same mutations, including the infamous E484K, appeared.

Such evidence adds to cautious optimism that mutations appear to share many of the same traits.

But the world must continue tracking changes in the virus, experts said, and choke off its ability to mutate by reducing transmission through vaccinations and measures that limit its spread.

“It’s shown a very strong set of opening moves,” Vaughn Cooper, an evolutionary biology specialist at the University of Pittsburgh School of Medicine, said of this coronavirus. “We don’t know what the end game is going to look like.”

Blast kills at least 13 in Pakistani city of Lahore, 83 injured

Police and rescue workers work at the scene of a blast in Lahore, Pakista

By Mubasher Bukhari

LAHORE, Pakistan (Reuters) – An explosion near the Punjab provincial assembly in the Pakistani city of Lahore killed at least 13 people and wounded 83 others on Monday, a senior police official said.

Mushtaq Sukhera, inspector general of police in Punjab province, said five police officers were among the dead when an explosion rocked a protest organized by Pakistan’s chemists and pharmaceuticals manufacturers.

“It was a suicide attack. The bomber exploded himself when successful negotiations were underway between police officials and the protesters,” Sukhera told reporters.

A spokesman for Jamaat-ur-Ahrar, a faction of the Pakistani Taliban, called Reuters and claimed responsibility.

The militant group also warned the Lahore attack was the start of a new campaign against government departments. “You are on our target across the country,” it added in a statement.

Jamaat-ur-Ahrar had also claimed responsibility for an Easter Day bombing in Lahore last year that killed more than 70 people in a public park.

Security in Pakistan has vastly improved in recent years but Islamist groups such as the Pakistani Taliban and Islamic State still pose a threat and have carried out mass attacks.

Prime Minister Nawaz Sharif said the attacks will not weaken Pakistan’s resolve in fight against militancy.

“We have fought this fight against the terrorists among us, and will continue to fight it until we liberate our people of this cancer, and avenge those who have laid down their lives for us,” he said in a statement.

The latest blast may jeopardize plans by Pakistan, a cricket-obsessed nation, to host the final of its domestic Twenty20 tournament on home soil in Lahore in March.

For years, Pakistan’s international test cricket matches have been played abroad and the current Twenty20 tournament is being played in United Arab Emirates due to security fears.

(Reporting by Mubasher Bukhari in Lahore; Additional reporting by Mehreen Zahra-Malik in Islamabad and Jibran Ahmad in Peshawar; Writing by Drazen Jorgic,; Editing by Tom Heneghan)

Brain Eating Amoeba Found in Louisiana Drinking Water

The Louisiana Department of Health and Hospitals has confirmed that the deadly brain-eating amoeba Naegleria fowleri was found in the drinking water of the St. Bernard Parish water system.

The parish has been asked to conduct a 60-day “chlorine burn” to kill off the amoeba.  The parish said they would comply “out of an abundance of caution.”

“At this point that’s a decision that the DHH has to make. We trust their expertise in this field. We do we feel that the system is fine and this was an anomaly,” said St. Bernard Parish President David Peralta.

“One positive test was at a site at the water treatment plant before the water was treated,” reads a statement from the DHH. “The second positive test occurred at 948 Angela Street, which may have been contaminated by ground water due to a leak at the sampling station.”

“Someone hit it. They probably hit it with a car or tractor or lawn mower-never reported it. It pocketed some water, so when they took the sample some of the standing water infiltrated our line. And that’s what gave us a positive indication,” said St. Bernard Parish President Dave Peralta.

The DHH says that the water is safe to drink, but that people should avoid getting water in their nose when bathing, washing or swimming because that’s the method the amoeba reaches the brain.  Only three people in the world since the discovery of the amoeba have survived an infection.

Meraux homeowner Ashley Jolly told WDSU she was shocked to get an alert about the amoeba in the middle of giving her twin boys a bath.

“They like to play in the water. And they just went through swimming lessons and they’re learning to blow water in and out of their nose and their mouths,” said Jolly.