Study: Stanford scientists find no COVID-19 infections in 2019 swabs

An analysis of 1,700 stored specimens from Bay Area-wide clinics detected no virus

As the Bay Area continues to tackle the COVID-19 pandemic, a mystery remains: When did the virus arrive here?

Speculation has been growing that the coronavirus may have been circulating in the region long before we knew it had reached our shores, but a new study suggests it wasn’t sickening people here in 2019.

Stanford University scientists announced on Tuesday that there’s no trace of the deadly virus in 1,700 throat swabs taken from sick people visiting Bay Area-wide clinics of Stanford Health Care in November and December, when the outbreak was exploding in China.

“No COVID-19 cases were identified, consistent with limited transmission in this population at this time,” reported investigator Dr. Catherine A. Hogan, an infectious diseases physician

“We can’t see the whole picture. This is one piece of the epidemic’s picture, but we’re not there yet.” — Dr. George Lemp, infectious disease epidemiologist

and medical microbiologist with Stanford’s Department of Pathology.

This doesn’t mean that the virus wasn’t here. Many cases of COVID-19 do not cause symptoms, so infected people may not have sought care from Stanford doctors.

But the study is the most thorough yet to mine a valuable repository of stored information in nasopharyngeal swab samples collected between Oct. 31 and Dec. 31, then stored.

The analysis offers an important snapshot in time. Like the Stanford team, researchers across the world are now poring over old medical specimens and reports hunting for clues of the start of the COVID-19 virus.

Scientists believe that finding “patient zero” will help them paint a wider, more accurate picture of the spread of the disease in its early stages, deepening our understanding of its transmission.

Once found, it could suggest that reports of winter fever, cough and unremitting phlegm were not just routine illnesses.

Until now, we’ve relied on reported cases and deaths to understand the origins of the outbreak. Testing by the U.S. Centers for Disease Control and Prevention didn’t start until Feb. 3, and it was very limited.

The origins of the Bay Area’s epidemic officially date back to Santa Clara County’s first recorded case on Jan. 31. Months later, the CDC and county public health officials revealed new tests showed a San Jose woman had become the nation’s first-known coronavirus-related

fatality on Feb. 6, suggesting the virus had been here earlier.

Yet such reported cases and deaths are only the tip of the iceberg of this large viral epidemic, said infectious disease epidemiologist Dr. George Lemp, former director of the California HIV AIDS Research Program at the University of California, who was not involved with this study but worked on several landmark “lookback studies” for the state’s first HIV infections.

“A lot more is hidden under the surface,” he said. “Scientists are trying to get some sense of the rest of it.”

Genetic analyses of the COVID-19 virus suggest it first emerged weeks, if not months, before the World Health Organization was notified of the original cluster of pneumonia cases associated with individuals who visited a wet market in Wuhan in the Hubei province

of China.

Officials in Wuhan confirmed the existence of a then-unknown illness with pneumonia-like symptoms to the World Health Organization’s China office on Dec. 31, but it wasn’t established as a new coronavirus until Jan. 7.

An unconfirmed report in the media indicated the diagnosis of a COVID-19 case in Hubei province on Nov. 17.

French doctors recently reexamined medical records of intensive care patients admitted for influenza-like illness between Dec. 2 and Jan. 16. This helped them establish the coronavirus was already present in Paris by late December — a month before the country’s first official recorded case and two and a half months before a nationwide lockdown.

Bay Area health officials were braced for early cases

here, because of our cultural and travel links to China. Santa Clara County Executive Jeff Smith, a medical doctor himself, has speculated the virus may have arrived in the county late last year and has been urging public health officials to explore the possibility.

The Stanford team’s retrospective study looked at nasopharyngeal swab samples collected last fall and winter at Stanford Health Care clinics — on the Peninsula and also in the East and South Bay — from patients admitted to hospitals or visiting doctors who were sick but tested negative for routine respiratory viruses. It was a preprint study — posted online, but not published in a scientific journal and not yet peer-reviewed.

Lemp, for one, isn’t surprised that none of them showed signs of coronavirus,

but he said that’s only part of the picture.

“It is limited to those persons seeking care at Stanford who were symptomatic,” Lemp said. “The vast majority of people with COVID-19 are asymptomatic. The chance that they would find a positive specimen — at a time when there was not much virus circulating — was quite low.”

As more data accumulates from other studies, we’ll gain a better understanding of the epidemic’s origins, he said.

“We are trying to paint a very careful picture of the scope of this viral epidemic. We have many different sources that each give us a snapshot,” said Lemp. “But we can’t see the whole picture. This is one piece of the epidemic’s picture, but we’re not there yet.”