Scientific Evidence of COVID19 Origins

The coronavirus that causes COVID19 is the stuff of science fiction. The virus transmits quickly, easily and when people don’t even know they’re infected. It’s no wonder no one notices what’s happening—until it’s too late. That’s part of the problem in trying to figure out how and where the coronavirus started. Increasingly, science provides evidence that the pandemic started much earlier than December 2019, it’s more widespread than the number of globally confirmed cases, and it most likely did not start in Wuhan.

Three kinds of scientific evidence

There are three kinds of scientific evidence that tease apart how the novel coronavirus—SARS-CoV-2—started: biological, epidemiological and genetic.

Biological: Wildlife with coronaviruses that can kill humans are found in global emerging disease ‘hotspots.’ One of these known ‘hotspots’ is southern China. Scientists largely agree that a bat coronavirus was involved in the zoonotic disease spillover of SARS-CoV-2 from animals to humans. Spillover is a common, naturally occurring event that has become more frequent in the 21st century. In fact, more than two-thirds of human viruses are zoonotic: think rabies or even measles. Often, zoonotic disease spillover involves more than one species. SARS-CoV-2 almost certainly is a mix of a bat coronavirus and another coronavirus found in pangolins (a tropical, scaled mammal illegally trafficked in wildlife markets). Scientists are looking into the possibility that a coronavirus from yet another animal was also involved.

Epidemiological: This new coronavirus is a wily operator. It is very different from other global disease threats we’ve experienced in the last 20 years, like Ebola in West Africa or the original 2003 SARS (Severe Acute Respiratory Syndrome) coronavirus epidemic. These diseases were quickly recognized—and acted upon—because of their dramatic symptoms and high mortality rates: 10% to 50% of infected people died. The new coronavirus is exactly the opposite. Most people don’t have dramatic symptoms. It doesn’t kill everyone it infects. Recent estimates suggest that 1% of people with COVID19 will die. That may not sound like a lot, but consider that the entire world has shut down and still COVID19 is spreading like wildfire. For comparison, during the 21-month Ebola epidemic in West Africa, 11,000 people died; in the five months since the new coronavirus was first reported, more than 380,000 have died. Ultimately, there will be millions more COVID19 cases than for any other lethal disease in modern history, with the possible exception of the 1918 Flu Pandemic.

A study by researchers at Northeastern University in Boston estimates that beginning in mid-January, more than 10,000 people in New York City were infected, before the first case of community acquired COVID19 was identified on March 1, 2020. Doctors in New York City were looking for COVID19, because they knew it would show up. Doctors in China were not looking for a novel coronavirus until increasing numbers of atypical pneumonia cases started showing up. If New York had 10,000 cases before they identified their first hospital case—and they were looking for COVID19—how many cases did China have before someone recognized that this was something new and dangerous?

Normally, when an outbreak occurs, there is an outbreak investigation. Infected people name all of their recent contacts, the infected contacts name their contacts and investigators go backwards in time to identify the first case. That is exactly what investigators did with the first 2003 SARS epidemic. They found that spillover had occurred in a live animal market. The problem this time around is that so many people were already infected by the time the outbreak was identified, it’s impossible to do traditional outbreak investigation.

Since the coronavirus was likely spreading months before it was identified, researchers around the world have been looking for evidence of earlier spread in their own countries. The US found an undetected, community acquired COVID19 case from mid-January. So did Brazil. France found evidence that COVID19 may have been circulating there as early as November of last year. Even China has backdated their first COVID19 case to mid-November, though genetic evidence suggests that SARS-CoV-2 was already circulating in China two months earlier.

Genetic: Some of the strongest scientific evidence about the origins of COVID19 comes from studies of virus genetics. Genetic evidence shows the changes and mutations that occur as the virus travels and infects people around the world. It shows a pathway of transmission. That’s how we know that the original cases of COVID19 on the west coast of the US came predominantly from China, while the original cases on the east coast mostly came from Europe.

To understand how the coronavirus started in China, Cambridge University researchers looked at the virus genetics from the first 160 COVID19 patients with virus genetic sequences. They identified three dominant strains: A, B and C. Then they did something that human geneticists don’t usually do. They added the virus genetics from the bat coronavirus most closely related to SARS-CoV-2 to their analysis. It’s not a perfect match between SARS-CoV-2 and the bat coronavirus—only 96%, room for animal coronaviruses to mix and recombine. This is much closer than the next nearest bat coronavirus relative, the original 2003 SARS coronavirus, which is an 80% match.

In their analysis, the Cambridge researchers found that Strain A was most closely related to the bat coronavirus. Strain B was two genetic mutations away from Strain A, and Strain C was the least related to the bat coronavirus. Then came the surprise. Strain A was found primarily in people from Guangdong Province, not in people from Wuhan. That makes a lot of sense. Guangdong Province is where the 2003 SARS coronavirus spillover occurred, and it is a well-documented emerging disease ‘hotspot’ where bats with coronaviruses can be found.

Even though the Cambridge study is based on small numbers, another team of international and Chinese researchers also suspect that the virus could have begun in Guangdong Province. They’ve been working together since February to conduct COVID19 tests on hospital specimens collected before anyone knew anything about this new coronavirus.

Although SARS-CoV-2 was officially reported by China on December 31, 2019, more than one genetic study suggests that the original spillover from animals to the human population probably happened as early as mid-September. That matters. It means that the virus could have been spreading uncontrollably for months, before it came to the attention of medical experts savvy enough to recognize a novel and dangerous pathogen. It also gave the virus a lot of time to hitch a ride outside of China and it helps explain how COVID19 is being found by researchers all over the world, well before the first medical cases were reported.

Science triumphs?

The truth is that we may never know the exact person who was first infected with COVID19 or even how it happened. Science will get us much closer to the truth. It’s pretty clear that SARS-CoV-2 came about through a complex but fairly common mixing of coronaviruses across species. It then spread like crazy—long before it was recognized—and led to the current pandemic. Pandemics are global. Only global scientific cooperation will help us end this one. The scientists are willing.

Originally publishedon June 3, 2020 here.