Friday, June 25, 2021

in-focus

A lab in Italy reported a cluster of the U.K. coronavirus variant. But that wasn't enough to stop the spread.


TERAMO, Italy - The virus hunter saw the apparent pattern come into view over several hours in late December, as he studied genetic sequences from positive coronavirus tests in his region. He found four cases involving the new, highly infectious British variant, in the same hilltop town.

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"A cluster," said Alessio Lorusso, the virologist.

His findings were a rare, initial insight into the mutated forms of the virus reaching new parts of the world. Most countries, including the United States and across Europe, do not perform enough genomic surveillance to adequately track the virus's changes - to the alarm of disease control agencies, which warn that governments could be blind to dangerous mutations.

But the scenario in Italy's mountainous center shows how even when a worrisome variant is detected early, governments can miss the narrow window to mount a rapid response and limit the spread. Containment measures come too late, in the wait for more substantial evidence. And the virus races ahead.

Lorusso's director quickly notified the affected region of the four cases. But it took more than two weeks for any official confirmation to reach the town of Guardiagrele and its population of 9,000. During that time, overall coronavirus cases there tripled, from 35 on Dec. 28 to more than 100 by mid-January. Of those, 29 have been confirmed to involve the British variant, compared with the 76 cases identified in the entire United States, where surveillance is highly lacking.

No targeted restrictions have been imposed on Guardiagrele or the surrounding region of Abruzzo, though there is a plan to soon perform widespread testing.

In Britain, the variant - known officially as B.1.1.7 - has forced a national lockdown, after the mutation defied regional measures that had curbed less transmissible strains. Though the variant appears responsive to vaccines and is not thought to be more deadly, it has spread so widely, and so overwhelmed hospitals, that it is causing the death toll to skyrocket, as well. In recent days, Britain has seen more per capita deaths than any other populous country, including the United States.

Scientists worry a similar escalation could follow elsewhere. On Friday, the Centers for Disease Control and Prevention warned the variant could become dominant in the United States by March. The timeline could be even shorter for some countries in Europe.

"If you don't act now, in two months, in all of Europe, we'll have the British variant taking the place of the current ones," said Walter Ricciardi, a World Health Organization adviser to Italy's Health Ministry.

He said that if a highly transmissible variant is detected in a particular place, it is important to act quickly, with widespread testing and restrictions on movement.

"You have to immediately lock down the area," Ricciardi said.

Virologist Alessio Lorusso oversees genetic analysis of coronavirus samples in Teramo, Italy. MUST CREDIT: photo for The Washington Post by Federica Valabrega.

To the extent that Italy has an early warning system, it depends on scientists such as Lorusso, 39, a bearded man who could pass for a retired wrestler outside the confines of his white-walled lab. He says he "likes viruses." He has spent much of the past year working 14-hour days, squinting at genomic code, watching SARS-CoV-2 evolve. The lab where he works, the Experimental Zooprophylactic Institute of Teramo, has now identified more than 50 instances of the British variant in the Abruzzo region. But the British variant is far from the dominant strain in the area.

"The variant with the greatest fitness will replace the others," he said. "It's just a fact."

For Lorusso and his lab, the British variant is fairly easy to hunt down. That's because it leaves a telltale: One of the most commonly used coronavirus testing machines, produced by the company Thermo Fisher, checks for the presence of three genes. In the British variant, one of those genes is missing. For somebody with the B.1.1.7 strain, the test result looks puzzling: positive-negative-positive.

Such a readout is hardly a definitive indication of B.1.1.7; some less concerning variants can yield a similar result. But it provides a starting point, and Lorusso's lab can then select swabs for deeper analysis.

Walking through the lab this past week, Lorusso stopped at the area where the swabs were being processed - 96 at a time, several thousand per day. In the room with the Thermo Fisher machine, he took a look at some recent test results - each corresponding to a person, who had been awaiting news of the outcome. In one batch of 96, nobody had the positive-negative-positive pattern. But in the next batch, 12 did.

Lorusso sat down at a computer, logging on to a system that tracks the personal information of everyone swabbed.

He checked for the home address of the one person who'd tested positive-negative-positive.

Guardiagrele.

He checked another.

Guardiagrele.

"Same neighborhood," he said.

He'd still have to sequence the code to know if it was B.1.1.7. But already, there was a growing number of newly arrived swabs revealing that same pattern.

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Italy reported its first detected case involving the British variant on Dec. 20, in a traveler who had arrived from Britain. The government in Rome stopped flights from the United Kingdom the same day.

But even by then, the variant was apparently already circulating in Italy.

Lorusso spotted the initial four cases from Guardiagrele - three within one family - on Dec. 26, and by Dec. 30, according to a document, the lab had informed regional government officials.

Regional officials, in turn, said they needed national government confirmation of the lab results. Into mid-January, the region was insisting there was still no "definitive proof" of a variant that might be spreading differently.

"The region never said to me, 'Dear mayor, there is a cluster in your town of the most infectious variant, so you'd better put a stop to everything,' " said Guardiagrele's mayor, Donatello Di Prinzio. "Had that been the case, I would have taken all the required actions."

Instead, after the end of a national holiday lockdown, all of Abruzzo - including his town - landed back in the lightest tier of Italian restrictions, with shops and hair salons open, and restaurants allowed to offered dine-in service until 6 p.m.

Meanwhile, coronavirus infections in the town were rising rapidly, reaching a point far exceeding anything from earlier waves. A local media report pointed to the variant, and there was speculation about it on Facebook. But without official word, the mayor said he didn't want to be alarmist.

"I only talk when there is data on my hand and official information," he said.

While he waited, Di Prinzio asked the region to send civil protection officers, who could supplement a depleted local police unit and help enforce basic distancing measures.

Then, on Tuesday, he was invited to a video conference with a provincial official and mayors from seven other towns that were seeing significant case increases. The authorities agreed to launch a mass-testing campaign in those towns, starting in Guardiagrele. It would kick off Jan. 23 - more than three weeks after Lorusso's initial findings.

One of the provincial officials involved with the health response, Giuseppe Torzi, said "measures need to be stricter" in places with the variant, but the crux of the response would be the same: try to isolate the positive cases and reduce contacts.

"I could list situations where there's no English variant and yet there's been a monstrous increase," Torzi said. "So it's not as if the other virus is some joke."

- - -

On Friday, Guardiagrele received definitive word of the variant's arrival, but not because of a national confirmation. Instead, Lorusso's lab notified the region, as well as a provincial health director, of updated, more extensive findings. Torzi called the mayor, feeling this time no further research was needed.

The province of Chieti, one portion of Abruzzo, had 51 cases of the variant.

Twenty-nine of those were in Guardiagrele.

That news coincided with a national government order that a large part of the country, including the Abruzzo region, would on the basis of infection rates be classified in the middle tier of coronavirus restrictions, which includes the closure of restaurants for in-person dining. Nonessential travel between regions will be banned through mid-February. But there has been no indication that Guardiagrele would be sealed off, as has happened in numerous hot spot Italian towns throughout the past year.

Speaking to The Washington Post by phone on Friday, Di Prinzio said he would redouble his request for residents to wear masks and keep their distance. He'd already closed a market. Nothing else would change. Even if he wanted to impose a lockdown, he said there was little point; other towns might well have the same problem, and it would have to be a coordinated effort.

Another lab doing genomic sequencing, at the University of Chieti, said it had traced a case in one town, San Giovanni Teatino, back to Guardiagrele, carried by a woman who works there.

"For such reason," the university wrote to the region, "it is possible to hypothesize that in these cases we are witnessing a progressive expansion of such a variant across the territory."

Lorusso, who said he had not been monitoring the policy response in the wake of his findings, said he realized people around the world were suddenly scrambling to understand the implications of this variant and others. He emphasized that even the most infectious strain could be curbed with rigorous distancing, mask-wearing and a reduction in social contact. Over the course of a day at the lab, he mentioned it so many times that he came to seem almost protective of the virus. The changes in SARS-CoV-2 were logical, not alarming, he said. The spread of the British variant, and any other highly infectious strains, depended on the behavior and decisions of humans.

"Viruses search for a host," he said. "It's human habits that make the pandemic."

Published : January 17, 2021

By : The Washington Post · Chico Harlan, Stefano Pitrelli