San Francisco Chronicle - (Sunday)
How virus shut down our world
New pathogen uniquely suited to ignite 21st century pandemic
On the last day of 2019, Dr. Yvonne Maldonado and her husband decided to drive up to San Francisco to celebrate. They were in their hotel on Union Square, getting ready for dinner on the seasonably cool and clearskied Tuesday night, when a news report on the television caught her attention.
It was a brief item, about a few cases of a mysterious pneumonia in China.
“And I thought, ‘ Oh no, the next SARS,’ ” Maldonado, an infectious disease expert at Stanford, recalled of that moment one year ago. Her thoughts had turned to the 2003 pandemic that infected 8,000 people and killed nearly 800 worldwide.
That thinking seems almost quaint now, with the global death toll from COVID19 above 1.8 million.
But on that last day of 2019, when Chinese
health authorities released the first public report of a curious disease that had sickened a couple of dozen people in Wuhan, even scientists like Maldonado had no idea what the new year would bring — that a novel virus would define 2020 and cause the most destructive pandemic in more than a century.
The coronavirus has infected more than 80 million people worldwide. It’s upended the global economy and forced dozens of countries into disorienting cycles of social and economic shutdowns. Millions of Americans have lost jobs from the fallout and cities across the country are facing unprecedented crises in business, housing, education and health.
Experts in infectious diseases and public health have come to understand that this coronavirus was uniquely suited to ignite a 21st century pandemic.
It is not the deadliest nor the most transmissible of pathogens, but it’s a stealthy germ, capable of causing widespread disease without notice. It’s deadly enough to warrant a fullscale public health defense, but it’s temperamental — sometimes striking with a lethal intensity that can afflict multiple organs, and sometimes inflicting no symptoms at all.
And this virus has thrived especially in the United States, taking advantage of a modern American culture that is politically and socially divided, spreading far and wide among a public prone to mistrust and doubtful of its leaders.
“We’re not in the kind of pandemic that we faced with black plague or smallpox or Spanish flu, which killed high fractions of the world’s population,” said Dr. Warner Greene, an infectious disease expert with the Gladstone Institutes, an independent research group in San Francisco. “This virus has had a paralyzing effect on the world. It has basically shut down country after country after country.”
And a year into the pandemic, the struggle is even more pronounced. “Even now, we are teetering on the edge,” Greene said.
Details in the first Chinese report were slim: 27 people with what appeared to be viral pneumonia, seven of them seriously ill. All of the initial cases were tied to a seafood market in Wuhan, a city of 11 million people in central China.
Scientists identified a new coronavirus as the culprit within weeks. It was named SARSCoV2 for “severe acute respiratory syndrome coronavirus 2,” a successor to the 2003 SARS virus. In February, the World Health Organization named the disease it causes COVID19, an acronym for “coronavirus disease 2019.” SARSCoV2 comes from a family of viruses that share a certain biology. Anatomically, coronaviruses’ most distinctive features are the “crown” of spiked proteins that cover their surface, giving the family its corona name. Those same spikes also are the key to how the new coronavirus infects humans, attaching to a protein called the ACE2 found on the surface of many important cells in the respiratory system, along with the heart and digestive tract.
Of the coronaviruses known to infect humans, several cause the common cold — they’re fairly easily spread but cause minor illness. Two coronaviruses, though, are standouts: They cause SARS and MERS, short for “MiddleEast respiratory syndrome,” alarmingly serious diseases that can kill up to 40% of those infected.
SARSCoV2, like most other coronaviruses, spent some unknown years or decades roosting quietly in animal hosts until it managed to mutate in such a way that it could infect humans, too. Scientists believe the new coronavirus circulated among bats, then moved into an intermediary animal — possibly pangolins, a type of scaled anteater — before hitting humans late last year.
Whatever its origin story, around the time the first people were infected in Wuhan, the new coronavirus developed the ability to pass easily from human to human, a critical adaptation.
“There are a lot of viruses that sort of ping humans, but they don’t get very far. Picking up the ability to transmit from human to human, that’s a very big deal,” said Shannon Bennett, chief of science at the California Academy of Sciences.
In the earliest days of this pandemic, she said, scientists and government leaders in China mistakenly assumed the new virus was “doing multiple animal to human events. They were not associating it with efficient human transmission,” she said.
By the time they realized that people weren’t being infected by animal contact but by other humans, “it was already too late,” Bennett said. “It had already adapted to efficient human to human transmission, and it was doing it gangbusters.”
SARSCoV2 is unlike all of its coronavirus siblings in several important ways. It can cause much more severe disease than a cold, but the COVID19 fatality rate is lower than SARS and MERS. It’s also much more infectious than the deadlier viruses.
Viruses like SARSCoV2 infect humans by breaking into cells and hijacking the engine by which they reproduce. The virus then uses that engine to replicate itself, spreading infection within the body.
This virus, Greene said, is especially productive. Early after people are infected they may already have high levels of the virus in their body, and the “dose” they can give to others when they come in contact is high, too.
“It just dominates the cell. It takes over the whole host machinery,” Greene said.
“This is a virus that’s designed for high efficiency and human spread.”
And perhaps most important, the new coronavirus passes from one person to another even when infected individuals have no symptoms. That’s not the case with SARS and MERS, which tend to spread when an infected person is very ill, coughing and sneezing virusladen droplets into the air.
“This virus spreads when people are asymptomatic or presymptomatic, so you never know who’s infected. There are no warning signs. You can’t just avoid the coughing person,” said Dr. Charles Chiu, director of viral diagnostics at UCSF. “You could be talking to your best friend and have no idea he’s infectious. This virus spreads in stealth mode.”
That trait makes the virus a tough foil for even the most robust public health systems.
Without cheap, nearunlimited access to rapid testing, people have to assume that anyone could be infectious at any time. Blanket public health mandates become critical, including universal masking, bans on all kinds of gatherings, and when cases are surging, broad economic shutdowns to compel people to stay home.
But those orders can be tough to enforce, especially when people have a hard time understanding that they could be spreading the virus even when they feel fine. People may mean well, they may respect the science and understand the reasoning behind the public health demands, but they still struggle to appreciate how their behavior may spread the virus in their community.
Even many infectious disease experts admit now that they were not as concerned early in the pandemic as they should have been. This new virus didn’t seem to cause as severe an illness as its SARS and MERS predecessors. And the world had managed to conquer both of those outbreaks.
“I think a number of people, myself included, incorrectly made analogies to SARS and MERS, because it is a similar coronavirus. But those diseases were, relatively speaking, easier to control, and get them back in their bottles,” said Dr. Art Reingold, head of the division of epidemiology at UC Berkeley.
“When we have a new infectious agent, all we can really do is make assumptions based on what we know, and make comparisons,” he said. “But they are dangerous. And those assumptions made this virus much more difficult to handle.”
Another unique feature of the new virus is the broad range of illness it can cause. Up to 40% of infected individuals may never have symptoms. A vast majority will
either have no symptoms or suffer illness similar to a bad cold or flu.
But the new coronavirus can kill roughly 1 in 100 people it infects, and it is far deadlier among the elderly and medically fragile. It’s much more serious than the seasonal flu, which kills about 40,000 people a year in the United States. The coronavirus killed more than 344,000 Americans in 2020.
In moresevere cases, the coronavirus can attack other organs besides the lungs, and it can trigger heart attacks and strokes. It can cause serious, longterm effects in a subset of people, perhaps 10% to 20% of those infected. These socalled longhaulers can suffer debilitating fatigue, headaches, body aches and other symptoms for months. Many seriously ill people also end up with mental health issues, either caused by the virus or the long, difficult treatment and recovery.
That vast spectrum of disease, especially in a climate of broad mistrust of science and government, has made it difficult to mount a united response. Younger people may not take it seriously because they are unlikely to die or even be seriously ill. Political leaders, including President Trump, have argued against dramatic shutdowns on the premise that the economic fallout is worse than the disease itself.
That’s left public health officials in the U. S. struggling to persuadepeople to make often unpalatable choices — skip Thanksgiving and Christmas with family, always wear masks in public — in order to curtail the spread of the disease.
“When the leadership does not come forward to recognize the seriousness of a virus, it allows it to spread and then it becomes more difficult to control,” said Dr. Jay Levy, an infectious disease expert at UCSF who was among the first scientists to identify the virus that causes AIDS in the 1980s.
This coronavirus, he said, was always going to be tough to manage. “China basically locked down the whole country and they’re still dealing with it,” he said. “When you have an agent that is spread in the air, it’s tough to control. You can’t tell people not to breathe. The public health measures are difficult to get people to adhere to.”
But the U. S. response was riddled by shocking missteps, Levy and other experts said, from national leaders refusing to admit the virus was a major threat to the rollout of flawed tests in the earliest weeks.
And while the government fumbled, the virus slipped into the country unnoticed and spread silently. Chiu and other infections disease experts believe the coronavirus probably came into the U. S. with travelers from China early in the pandemic, maybe in December and definitely by January.
By the time authorities had the tools and the awareness to look for it at the end of February, the virus had a foothold in half a dozen regions, including the Bay Area. That’s when the first shutdowns became necessary, and 2020 went wildly awry.
“In California, we are very entrenched in a massive endemic process,” said Maldonado. The virus is well established in communities around the state, with more than 40,000 new cases reported daily. And while those numbers can be pushed down, the virus can no longer be banished without a vaccine.
But ultimately, the traits that made this virus so perfectly primed to sweep over the globe also make it too dangerous to survive, said Dr. Robert Siegel, a virologist at Stanford. It’s too deadly and too infectious for the world to not fight back — with vaccines developed at a record pace.
“That will be its downfall,” Siegel said, “the fact that it got us all riled up.”