San Diego became the first community in the state, and one of the first in the country, to detect the presence of a new variant of the new coronavirus, announcing that a local man in his 30s had tested positive for the strain on Tuesday.
Confirmed by a quick genetic analysis at 3 am on Wednesday, the case signals the presence of the same pathogen that has taken three quarters of England’s population – about 40 million people – to the strictest level of that country’s blockade system.
The new strain of the virus appears to be able to spread more quickly than other circulating versions.
The San Diego case is among three known or suspected to be of the United Kingdom subtype, called B.1.1.7. Media reports indicate that two National Guard members stationed in Colorado also have the same type of infection. As of Wednesday night, one had been confirmed while confirmation was still pending for the second.
Dr. Eric McDonald, medical director of the county’s epidemiology department, said the San Diego resident did not report any trips abroad before he became ill and neither case in Colorado. The travel history was not yet available for the second.
In the absence of travel evidence, it appears that those with confirmed infections have contracted the virus in their communities, strongly suggesting that the UK strain is more widespread in the community than people realize.
“There are other cases in San Diego that we need to be aware of,” said McDonald.
The San Diego affair seems to have listened to the current order to stay at home.
“Going back two weeks, the number of activities was also very limited,” said McDonald. “There was no work activity and there was no specific collection activity that we said was the potential for an outbreak in the community.”
Scientists around the world are struggling to learn as much as they can about B.1.1.7. and another similar strain detected in South Africa that appears to have a similar turbocharged transmission capacity.
Wednesday was busy in terms of COVID developments.
On Wednesday, San Diego Mayor Todd Gloria announced a new executive order that calls for stricter enforcement of health orders. San Diego law enforcement officers, Gloria said, must now work with the city’s attorney’s office to more aggressively pursue $ 1,000 fines for those who “blatantly and flagrantly challenge the provision of state and municipal public health orders.”
Sharp HealthCare, the region’s largest health care system, has also come under scrutiny for administering 300 doses of coronavirus vaccine for local first aid. Police and firefighters are not at the top level of the state’s vaccination prioritization program, which says doses should go to frontline health workers and nursing home residents and staff.
In an email, a Sharp employee said that the doses, which are kept for up to six months in deep freezing, were about to expire, having almost reached the end of the five-day viability period after they were thawed and prepared to be used in a vaccination clinic for Sharp employees.
Sharp said he is rethinking his planning process for managing vaccines used in mobile clinics. So far, about 10,000 of the 20,000 doses Sharp has received have been used.
San Diego is one of the first communities in the country to detect the UK strain, probably because its biomedical community has apparently been paying close attention to information coming in from the UK since the new version of the virus was announced in early December. The researchers noted that a specific COVID molecular test by the giant Thermo Fisher, which targets three different spots in the genome of the COV2 virus, has a fortuitous ability to signal that a coronavirus may be of the UK type.
The UK variant is known to have a mutation that excludes a small portion of its S gene, the one that determines the shape of the distinct proteins on the peak surface that give it its name.
Since the Thermo Fisher test targets three different locations, it is still possible to get a positive with only two of the three combined. The results that return with two hits and a failure in the S gene target, therefore, are possibly of the United Kingdom variant. However, other mutated versions of the virus also exclude the same target from the S gene, so genetic sequencing is necessary as a second step to confirm that the virus involved is in fact B.1.1.7.
This whole sequence happened very quickly in San Diego with the UC San Diego EXCITE laboratory detecting the S drop and immediately forwarding a sample to Scripps Research immunologist and molecular biologist Kristian Andersen, whose laboratory worked overnight to answer the question, delivering a result in the early hours of the morning.
Speaking at the county COVID-19 weekly news conference on Wednesday afternoon, Andersen warned that, as has been the case in the UK, the variant is probably already among us. He called for a rededication to hand washing practices, wearing masks and social detachment that have decreased in recent months, as many complain of COVID-19 fatigue.
“Detecting that strain here doesn’t really change what we need to do, unless we need to do better,” said Andersen.
He said that no one is sure whether the UK variant will be as easily transmissible in southern California as it appears to be the case in England.
“We should expect the same thing to happen here in San Diego, but we still don’t know if that will really be the case,” he said.
The UC San Diego EXCITE laboratory has processed about 1,000 samples per day, determining whether they are positive or negative. The samples were taken from students, teachers and school staff, as well as some public schools in San Diego County and the San Diego Fire and Rescue.
It was not clear on Wednesday whether the person who tested positive had any direct connection to UCSD.
“We are determining whether the variant came from a student or someone else,” said Dr. David Brenner, vice president of health sciences at UC San Diego.
Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, said he was very familiar with the work of Andersen, who has earned a national and international reputation. Detecting the variant so quickly, he said, is probably a harbinger of things to come. Although science centers like San Diego are usually the first to detect these arrivals, the fact that no one has reported travel abroad so far means that there is more of the same out there waiting to be found.
“I think this virus was probably spread across much of the United States,” he said.
It must, he added, be a worrying reminder that this is not the year for a big New Year’s Eve party.
“Celebrate with those you love who you were in the same bubble of exposure with,” he said. “The greatest gift you can give them is that they are not exposed to this virus, so that they can be around on New Year’s Eve 2021.”